We will continue to develop this. Initially this will primarily be a file with a set of functions. We will work to turn this into a package and submit it to a repository.
Check for updates frequently we will try to update along with new REST API functions.
As downloaded this will call the production REST API version
(https://rest.phenogen.org).
Please use this for all analysis. You are welcome to use the development
and test version, by changing the phenogenURL variable to
(https://rest-test.phenogen.org), but please only use this for testing
and please be aware the rate of calls allows is more limited.
New functions that haven't been deployed to production will appear in testing first and will be implemented in development branch first.
getDatasetExpression( annotation ,level,tissue,version="",genomeVersion="",strainMeans=FALSE, help) - returns a dataframe containing the most recent expression data table matching the annotation["Ensembl","Reconstruction"], level=["Gene","Transcript"],and tissue["Brain","Liver","Heart","Kidney"]. If you specify any version or genomeVersion the version or most recent version matching those criteria will be selected. It will default to individual values, but by specifying strainMeans=TRUE you can get a dataFrame of strain means.
brainGeneExpression=getDatasetExpression(annotation="Ensembl",level="Gene",tissue="Brain")
| geneID | ACI_1_batch11 | ACI_2_batch10 | ACI_3_batch8 | BN_1_batch16 | BN_2_batch17 | BN_3_batch17 | BNLx_1_batch3 | ... |
|---|---|---|---|---|---|---|---|---|
| ENSRNOG00000000001 | 5.4926754 | 5.4582437 | 5.4799894 | 5.4593561 | 5.6670520 | 5.5736410 | 5.523891 | ... |
| ENSRNOG00000000007 | 13.4155761 | 13.2379013 | 13.4139346 | 13.3752669 | 13.6202354 | 13.4379441 | 13.095286 | ... |
| ENSRNOG00000000008 | 4.5838578 | 4.0120344 | 4.0284626 | 4.0093282 | 4.0500272 | 4.2187905 | 3.505616 | ... |
| ENSRNOG00000000010 | 11.3641079 | 10.8430474 | 11.3009947 | 11.3939719 | 11.2973067 | 11.4022849 | 11.410452 | ... |
| ENSRNOG00000000012 | 4.2356596 | 4.1371101 | 3.7849114 | 4.3626185 | 4.2039562 | 4.1742752 | 4.219597 | ... |
| ENSRNOG00000000017 | 5.7874644 | 6.2132814 | 5.7661025 | 5.3906472 | 5.3842575 | 5.6754122 | 5.381001 | ... |
getDatasetExpressionTPM( annotation ,level,tissue,version="",genomeVersion="",strainMeans=FALSE, help) - returns a dataframe containing the most recent expression data table containing TPM values matching the annotation["Ensembl","Reconstruction"], level=["Gene","Transcript"],and tissue["Brain","Liver","Heart","Kidney"]. If you specify any version or genomeVersion the version or most recent version matching those criteria will be selected. It will default to individual values, but by specifying strainMeans=TRUE you can get a dataFrame of strain means.
brainGeneExpressionTPM=getDatasetExpressionTPM(annotation="Ensembl",level="Gene",tissue="Brain")
| geneID | ACI_1_batch11 | ACI_1_batch8 | ACI_2_batch10 | ACI_2_batch8 | ACI_3_batch8 | BN_1_batch16 | BN_2_batch17 | ... |
|---|---|---|---|---|---|---|---|---|
| ENSRNOG00000000001 | 0.06 | 0.00 | 0.08 | 0.07 | 0.09 | 0.07 | 0.21 | ... |
| ENSRNOG00000000007 | 13.73 | 7.90 | 18.07 | 10.82 | 20.76 | 20.92 | 50.75 | ... |
| ENSRNOG00000000008 | 0.27 | 0.00 | 0.12 | 0.22 | 0.09 | 0.05 | 0.11 | ... |
| ENSRNOG00000000009 | 0.01 | 0.00 | 0.00 | 0.07 | 0.00 | 0.00 | 0.00 | ... |
| ENSRNOG00000000010 | 1.64 | 2.17 | 1.02 | 0.91 | 1.48 | 6.53 | 14.14 | ... |
| ENSRNOG00000000012 | 0.14 | 0.53 | 0.16 | 0.10 | 0.06 | 0.29 | 0.32 | ... |
getDatasets( genomeVer, organism, panel, type, tissue, help) - returns a dataframe containing a list of datasets available. If you specify any parameters it will filter the list based on the parameters. (type must be either "totalRNA" or "smallRNA")
phenoGenDatasets=getDatasets()
| datasetID | organism | panel | description | created | tissue | SeqType | GenomeVer |
|---|---|---|---|---|---|---|---|
| 3 | Mm | ILS/ISS | Whole Brain from ILS/ISS Parental Strains | 2017-10-26 00:00:00 | Whole Brain | smallRNA | mm10 |
| 4 | Mm | ILS/ISS Panel | Whole Brain from ILS/ISS RI Panel | 2017-10-30 00:00:00 | Whole Brain | smallRNA | mm10 |
| 5 | Rn | HRDP | HRDP v5 Whole Brain 45 Strains | 2020-06-20 00:00:00 | Whole Brain | ribosome depleted totalRNA | rn6 |
| 6 | Rn | HRDP | HRDP v5 Liver 45 Strains | 2020-06-20 00:00:00 | Liver | ribosome depleted totalRNA | rn6 |
| 7 | Rn | HRDP | HRDP v5 Kidney 28 Strains | 2020-06-20 00:00:00 | Kidney | ribosome depleted totalRNA | rn6 |
| 8 | Rn | HRDP | HRDP v5 Heart BNLx/SHR | 2021-08-07 00:00:00 | Heart | ribosome depleted totalRNA | rn6 |
getDatasetResults( datasetID, help ) - returns a list of results for the
dataset.
Results reflect different types of data, transcriptome reconstruction,
RSEM results on a specific version of the transcriptome. From the
results you can request a list of files( getDatasetResultFiles() ).
phenoGenDataset=getDatasetResults(datasetID=6)
| resultID | type | genomeVersion | hrdpVersion | dateCreated |
|---|---|---|---|---|
| 5 | Quantification-RSEM - Ensembl | rn6 | 5 | 2020-06-20 00:00:00 |
| 6 | Transcriptome Reconstruction | rn6 | 5 | 2020-06-20 00:00:00 |
| 7 | Quantification-RSEM - Reconstruction | rn6 | 5 | 2020-06-20 00:00:00 |
getDatasetResultFiles( datasetID, resultID, help ) - returns a list of files for the dataset/result specified. The results include the URL to download the file and can be given to getDatasetResultFile() to load the file into R.
phenoGenDatasetFiles=getDatasetResultFiles(datasetID=6,resultID=7)
| fileID | uploadDate | fileName | URL | checksum | genomeVersion | description | annotation | level | strainMeans |
|---|---|---|---|---|---|---|---|---|---|
| 15 | 2020-06-20 00:00:00 | PhenoGen.HRDP.v5.totalRNA.Liver.gene.reconstruction.strainMeans.txt.gz | https://phenogen.org/downloads/RNASeq/RSEM/PhenoGen.HRDP.v5.totalRNA.Liver.gene.reconstruction.strainMeans.txt.gz | 339492503250921c1e12f062fd538598 | rn6 | NA | Reconstruction | Gene | TRUE |
| 16 | 2020-06-20 00:00:00 | PhenoGen.HRDP.v5.totalRNA.Liver.transcript.reconstruction.strainMeans.txt.gz | https://phenogen.org/downloads/RNASeq/RSEM/PhenoGen.HRDP.v5.totalRNA.Liver.transcript.reconstruction.strainMeans.txt.gz | 8f2fa86774aed5602432ba20a898f116 | rn6 | NA | Reconstruction | Transcript | TRUE |
| 19 | 2020-06-20 00:00:00 | PhenoGen.HRDP.v5.totalRNA.Liver.gene.reconstruction.txt.gz | https://phenogen.org/downloads/RNASeq/RSEM/PhenoGen.HRDP.v5.totalRNA.Liver.gene.reconstruction.txt.gz | e7f4a4ef7d3aa94db0323abcbf7bd1f1 | rn6 | NA | Reconstruction | Gene | FALSE |
| 20 | 2020-06-20 00:00:00 | PhenoGen.HRDP.v5.totalRNA.Liver.transcript.reconstruction.txt.gz | https://phenogen.org/downloads/RNASeq/RSEM/PhenoGen.HRDP.v5.totalRNA.Liver.transcript.reconstruction.txt.gz | fad306dc42914bd071556b65f45f8eae | rn6 | NA | Reconstruction | Transcript | FALSE |
getDatasetResultFile( URL ) - tries to read a table from the given file and return the dataframe. It does support gzipped files and unzipped files. Currently it assumes tab delimited for anything other than .csv. It will change the delimiter if the file ends in .csv.
phenoGenData=getDatasetResultFile(URL="https://phenogen.org/downloads/RNASeq/RSEM/PhenoGen.HRDP.v5.totalRNA.Liver.gene.reconstruction.strainMeans.txt.gz")
| ACI.SegHsd | BNLx | BXH10 | BXH11 | BXH12 | BXH13 | BXH2 | BXH3 | BXH5 | BXH6 | BXH8 | BXH9 | Cop.CrCrl | DA | F344.NCl | F344.NHsd | F344.Stm | HXB1 | HXB10 | HXB13 | HXB15 | HXB17 | HXB18 | HXB2 | HXB20 | HXB21 | HXB22 | HXB23 | HXB24 | HXB25 | HXB27 | HXB29 | HXB3 | HXB31 | HXB4 | HXB5 | HXB7 | LE.Stm | LEW.Crl | LEW.SsNHsd | SHR | SHRSP | SR | SS | WKY | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| PRN6.5G0000002 | 2.471885 | 2.843376 | 2.988058 | 2.008068 | 2.803343 | 3.226419 | 2.690378 | 2.929471 | 2.899790 | 2.443884 | 2.979799 | 3.013484 | 3.344496 | 3.232358 | 3.859046 | 3.642551 | 3.162583 | 2.990749 | 3.571474 | 3.218356 | 2.849306 | 3.283459 | 3.291732 | 2.895224 | 2.301590 | 2.735003 | 3.224193 | 3.818431 | 2.636773 | 2.314870 | 3.309808 | 2.427989 | 2.829324 | 4.047287 | 3.250463 | 2.388294 | 2.550821 | 2.800644 | 2.594503 | 2.753139 | 2.611620 | 3.154226 | 3.356459 | 2.359043 | 2.032995 |
| PRN6.5G0000018 | 7.972751 | 7.988188 | 8.327635 | 7.483179 | 8.308570 | 8.493277 | 7.656435 | 8.034155 | 7.419229 | 7.744099 | 7.772140 | 7.879737 | 8.892710 | 8.674106 | 8.926560 | 8.524224 | 9.830253 | 7.921848 | 7.782879 | 8.230908 | 7.810042 | 7.817220 | 7.938246 | 7.742655 | 7.662234 | 7.349877 | 7.665480 | 8.443167 | 7.403185 | 7.390368 | 8.295641 | 7.716124 | 7.821002 | 8.286780 | 7.841284 | 8.102923 | 7.772143 | 8.351444 | 8.188147 | 8.261466 | 7.580521 | 8.472662 | 8.664102 | 9.273093 | 7.726402 |
| PRN6.5G0000023 | 3.635240 | 3.919247 | 4.123028 | 3.633602 | 4.865721 | 4.749075 | 4.191927 | 3.862219 | 3.688691 | 4.015154 | 3.978780 | 4.069461 | 4.312069 | 4.604477 | 4.507873 | 3.462370 | 4.377501 | 4.080252 | 4.425630 | 4.695526 | 4.251516 | 4.135177 | 4.516254 | 3.947551 | 4.046057 | 3.536359 | 4.247595 | 4.381584 | 3.699361 | 3.071000 | 4.919601 | 4.383471 | 4.343141 | 4.698016 | 4.225777 | 4.241549 | 4.812240 | 4.069986 | 4.749160 | 3.400256 | 3.408126 | 3.401887 | 3.625541 | 5.008848 | 3.008453 |
| ... |
getDatasetGTF( URL, splitIDColumn=FALSE, select="ALL" ) - can be used for GTF files instead of getDatasetResultFile() splitting the ID(9th) column or filtering for just exons or transcripts is desired.
The options can be used seperately or together.
-
splitIDColumn - indicates if the 9th column of additional annotations should be split into multiple columns. Currently this is limited to 2 columns Gene and Transcript.
-
select - can be used to filter rows to contain only: transcripts (select="TRANSCRIPTS") or exons (select="EXONS")
getDatasetSamples( datasetID, help ) - creates a table of sample details from the metadata of the dataset.
getDatasetPipelineDetails( datasetID, help ) - creates a table of pipelines used to process the data in the results. Each pipeline has steps associated with it that can be viewed that can include the programs used with versions, URL for the program, and even the command line used if provided.
getDatasetProtocolDetails( datasetID, help ) - creates a table of protocols used in the library preparation. Beyond title and description details are provided as a download. When available the URL will be provided to download the protocol used. Further detail not yet provided can include notes on individual samples.
getMarkerSets( genomeVer="",organism="" ) - returns a dataFrame of MarkerSets available.If a genomeVer or organism is specified then it will return matching datasets.
phenoGenMarkerSets=getMarkerSets()
| download_group_id | display_name | organism | genome_version | panel | description | type |
|---|---|---|---|---|---|---|
| 1 | HRDPv6 Markers | Rat | rn7.2 | HRDP | HRDP v6 markers from strain sequencing variant calls | Marker |
| 2 | HRDPv4 Markers | Rat | rn6 | HRDP | STAR Consortium Genotype Arrays ( http://oct2012.archive.ensembl.org/Rattus_norvegicus/Info/Content?file=star.html ) | Marker |
| 3 | HXB/BXH Markers | Rat | rn5 | HXB/BXH | STAR Consortium Genotype Arrays ( http://oct2012.archive.ensembl.org/Rattus_norvegicus/Info/Content?file=star.html ) | Marker |
| 4 | BXD Markers | Mouse | mm9 | BXD | Wellcome-CTC Mouse Strain SNP Genotype Set | Marker |
| 5 | LXS Markers | Mouse | mm10 | LXS | Affymetrix Mouse Diversity SNP Array | Marker |
getMarkerFiles( markerSetID, help )- returns a dataFram with a list of marker set files available.
phenoGenMarkerFiles=getMarkerFiles(markerSetID=1)
| download_file_id | marker_set_id | description | filename | checksum | URL |
|---|---|---|---|---|---|
| 1 | 1 | HRDPv6 Marker Genotypes | HRDP.v6.rn7.genotypes.2023-01-17.txt.gz | 110da4cb07901b7e8fcec0778d89a141 | https://phenogen.org/web/sysbio/downloadLink.jsp?url=/downloads/Markers/HRDP.v6.rn7.genotypes.2023-01-17.txt.gz |
| 2 | 1 | HRDPv6 Marker Positions | HRDP.v6.rn7.positions.2023-01-17.txt.gz | 22e76bcdb6a8b4aa6cf75ea73f969bd1 | https://phenogen.org/web/sysbio/downloadLink.jsp?url=/downloads/Markers/HRDP.v6.rn7.positions.2023-01-17.txt.gz |
getMarkerFile( URL, help ) - returns a dataFrame with the marker set file contents.
phenogenMarkerData=getMarkerFile(URL="https://phenogen.org/web/sysbio/downloadLink.jsp?url=/downloads/Markers/HRDP.v6.rn7.genotypes.2023-01-17.txt.gz")
| BN.Lx_Cub_mRatNor1 | BXH10_mRatNor1 | BXH11_mRatNor1 | BXH12_mRatNor1 | BXH13_mRatNor1 | BXH2_mRatNor1 | BXH3_mRatNor1 | BXH5_mRatNor1 | BXH6_mRatNor1 | BXH8_mRatNor1 | BXH9_mRatNor1 | HXB1_mRatNor1 | HXB10_mRatNor1 | HXB13_mRatNor1 | HXB15_mRatNor1 | HXB17_mRatNor1 | HXB18_mRatNor1 | HXB2_mRatNor1 | HXB20_mRatNor1 | HXB21_mRatNor1 | HXB22_mRatNor1 | HXB23_mRatNor1 | HXB24_mRatNor1 | HXB25_mRatNor1 | HXB27_mRatNor1 | HXB29_mRatNor1 | HXB3_mRatNor1 | HXB31_mRatNor1 | HXB4_mRatNor1 | HXB5_mRatNor1 | HXB7_mRatNor1 | SHR_OlaIpcv_mRatNor1 | ACI_EurMcwi_2019NOV | BN_NHsdMcwi_2019 | BUF_N_2020 | DA_OlaHsd_2019NOV | F344_NCrl_2019NOV | F344_NHsd_2021 | F344_Stm_2019 | FHH_EurMcwi_2019NOV | FXLE12_Stm_2019NOV | FXLE13_Stm_2019NOV | FXLE14_Stm_2019NOV | FXLE15_Stm_2019NOV | FXLE16_Stm_2019 | FXLE17_Stm_2019NOV | FXLE18_Stm_2019 | FXLE20_Stm_2019NOV | GK_FarMcwi_2019NOV | LE_Stm_2019 | LEW_Crl_2019 | LXF10A_StmMcwi_2020 | LEXF11_Stm_2020 | LEXF1A_Stm_2019 | LEXF1C_Stm_2019 | LEXF2B_Stm_2019 | LEXF3_Stm_2020 | LEXF4_Stm_2020 | LEXF5_Stm_2019NOV | LEXF6B_Stm_2019NOV | LEXF6B_Stm_2021_A | LEXF6B_Stm_2021_BH | LEXF6B_Stm_2021_FH | LEXF7A_Stm_2019NOV | LEXF8A_Stm_2021 | LH_MavRrrcAek_2020 | LL_MavRrrcAek_2020 | LN_MavRrrcAek_2020 | M520_N_2020 | MR_N_2020 | MWF_Hsd_2019NOV | PVG_Seac_2019 | RCS_LavRrrc_2021 | SHR_NCrl_2021 | SHRSP_A3NCrl_2019NOV | SR_JrHsd_2020 | SS_JrHsd_2021 | WAG_RijCrl_2020 | WKY_N_2020 | WKY_NCrl_2019 | WN_N_2020 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| chr1_16211 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 2 | 2 | 0 | 2 | 0 | 2 | 2 | 0 | 2 | 0 | 2 | 0 | 0 | 0 | 2 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| chr1_17226 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 2 | 2 | 0 | 2 | 0 | 2 | 2 | 0 | 2 | 0 | 2 | 0 | 0 | 0 | 2 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| chr1_17294 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 2 | 2 | 0 | 2 | 0 | 2 | 2 | 0 | 2 | 0 | 2 | 0 | 0 | 0 | 2 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
filterGTF( gtfDataFrame, splitIDColumn=FALSE, select="ALL" ) - can be used on the dataFrame returned from getting a GTF. The options can be used seperately or together. splitIDColumn - indicates if the 9th column of additional annotations should be split into multiple columns. Currently this is limited to 2 columns Gene and Transcript. select - can be used to filter rows to contain only: transcripts (select="TRANSCRIPTS") or exons (select="EXONS")
phenoGenDatasets=getDatasets()
View(phenoGenDatasets)
| datasetID | organism | panel | description | created | tissue | SeqType | GenomeVer |
|---|---|---|---|---|---|---|---|
| 3 | Mm | ILS/ISS | Whole Brain from ILS/ISS Parental Strains | 2017-10-26 00:00:00 | Whole Brain | smallRNA | mm10 |
| 4 | Mm | ILS/ISS Panel | Whole Brain from ILS/ISS RI Panel | 2017-10-30 00:00:00 | Whole Brain | smallRNA | mm10 |
| 5 | Rn | HRDP | HRDP v5 Whole Brain 45 Strains | 2020-06-20 00:00:00 | Whole Brain | ribosome depleted totalRNA | rn6 |
| 6 | Rn | HRDP | HRDP v5 Liver 45 Strains | 2020-06-20 00:00:00 | Liver | ribosome depleted totalRNA | rn6 |
| 7 | Rn | HRDP | HRDP v5 Kidney 28 Strains | 2020-06-20 00:00:00 | Kidney | ribosome depleted totalRNA | rn6 |
| 8 | Rn | HRDP | HRDP v5 Heart BNLx/SHR | 2021-08-07 00:00:00 | Heart | ribosome depleted totalRNA | rn6 |
phenoGenDataset=getDatasetResults(datasetID=5)
View(phenoGenDataset)
| resultID | type | genomeVersion | hrdpVersion | dateCreated |
|---|---|---|---|---|
| 2 | Quantification-RSEM - Ensembl | rn6 | 5 | 2020-06-20 00:00:00 |
| 3 | Transcriptome Reconstruction | rn6 | 5 | 2020-06-20 00:00:00 |
| 4 | Quantification-RSEM - Reconstruction | rn6 | 5 | 2020-06-20 00:00:00 |
4. Find the resultID of the results that you would like to load typical options are typically Ensembl, RefSeq, or Reconstructed Transcriptomes: - resultID = 4 for Expression values of the reconstructed transcriptome.
phenoGenDatasetResults=getDatasetResultFiles(datasetID=5,resultID=4)
View(phenoGenDatasetResults)
| fileID | uploadDate | fileName | URL | checksum | genomeVersion | description | annotation | level | strainMeans |
|---|---|---|---|---|---|---|---|---|---|
| 6 | 2020-06-20 00:00:00 | PhenoGen.HRDP.v5.totalRNA.Brain.gene.reconstruction.strainMeans.txt.gz | https://phenogen.org/downloads/RNASeq/RSEM/PhenoGen.HRDP.v5.totalRNA.Brain.gene.reconstruction.strainMeans.txt.gz | 14201681cbd5996dca0ad0c44562ea12 | rn6 | NA | Reconstruction | Gene | TRUE |
| 7 | 2020-06-20 00:00:00 | PhenoGen.HRDP.v5.totalRNA.Brain.transcript.reconstruction.strainMeans.txt.gz | https://phenogen.org/downloads/RNASeq/RSEM/PhenoGen.HRDP.v5.totalRNA.Brain.transcript.reconstruction.strainMeans.txt.gz | b463a647ae9150eade8a1459a72fafc2 | rn6 | NA | Reconstruction | Transcript | TRUE |
| 10 | 2020-06-20 00:00:00 | PhenoGen.HRDP.v5.totalRNA.Brain.gene.reconstruction.txt.gz | https://phenogen.org/downloads/RNASeq/RSEM/PhenoGen.HRDP.v5.totalRNA.Brain.gene.reconstruction.txt.gz | 142ecc3eb16b1d8adae60d6709948ba0 | rn6 | NA | Reconstruction | Gene | FALSE |
| 11 | 2020-06-20 00:00:00 | PhenoGen.HRDP.v5.totalRNA.Brain.transcript.reconstruction.txt.gz | https://phenogen.org/downloads/RNASeq/RSEM/PhenoGen.HRDP.v5.totalRNA.Brain.transcript.reconstruction.txt.gz | c238dcb839fdae5acb384eef9c430592 | rn6 | NA | Reconstruction | Transcript | FALSE |
6. Copy the URL of the file you would like to load. Options usually include gene level or transcript level quantification and individual samples or strain means. - https://phenogen.org/downloads/RNASeq/RSEM/PhenoGen.HRDP.v5.totalRNA.Brain.gene.reconstruction.txt.gz for Gene Level individual samples on the reconstructed transcriptome.
BrainGeneReconstruction=getDatasetResultFile(URL="https://phenogen.org/downloads/RNASeq/RSEM/PhenoGen.HRDP.v5.totalRNA.Brain.gene.reconstruction.txt.gz")
View(BrainGeneReconstruction)
| Cop.CrCrl_1_batch9 | SS_2_batch8 | SR_2_batch8 | SR_1_batch8 | SHRSP_3_batch8 | LEW.Crl_3_batch8 | F344.NCl_3_batch8 | DA_3_batch8 | Cop.CrCrl_3_batch8 | ACI.SegHsd_3_batch8 | HXB31_2_batch7 | HXB29_2_batch7 | BXH9_3_batch7 | BXH8_4_batch7 | BXH6_3_batch7 | BXH5_2_batch7 | BXH3_3_batch7 | BXH2_2_batch7 | BXH11_3_batch7 | BXH10_3_batch7 | SHR_3_batch6 | HXB27_3_batch6 | HXB25_3_batch6 | HXB24_3_batch6 | HXB24_2_batch6 | HXB23_3_batch6 | HXB23_2_batch6 | HXB22_3_batch6 | HXB22_2_batch6 | HXB21_3_batch6 | HXB21_2_batch6 | HXB20_3_batch6 | HXB20_2_batch6 | HXB2_3_batch6 | HXB18_3_batch6 | HXB18_2_batch6 | HXB17_3_batch6 | HXB1_2_batch6 | BXH13_3_batch6 | BXH13_2_batch6 | BXH12_3_batch6 | HXB7_3_batch5 | HXB5_3_batch5 | HXB5_2_batch5 | HXB4_3_batch5 | HXB4_2_batch5 | HXB3_3_batch5 | HXB3_2_batch5 | HXB15_3_batch5 | HXB15_2_batch5 | HXB13_3_batch5 | HXB10_3_batch5 | HXB10_2_batch5 | HXB1_3_batch5 | BXH9_2_batch3 | BXH9_1_batch3 | BXH8_1_batch3 | BXH6_2_batch3 | BXH6_1_batch3 | BXH5_1_batch3 | BXH3_2_batch3 | BXH3_1_batch3 | BXH13_1_batch3 | BXH11_2_batch3 | BXH11_1_batch3 | BXH10_2_batch3 | BXH10_1_batch3 | BNLx_2_batch3 | BNLx_1_batch3 | HXB5_1_batch2 | HXB4_1_batch2 | HXB31_1_batch2 | HXB3_1_batch2 | HXB29_1_batch2 | HXB24_1_batch2 | HXB23_1_batch2 | HXB22_1_batch2 | HXB21_1_batch2 | HXB20_1_batch2 | HXB18_1_batch2 | HXB15_1_batch2 | HXB10_1_batch2 | HXB1_1_batch2 | BXH2_1_batch2 | WKY_3_batch11 | SS_3_batch11 | SR_3_batch11 | LEW.SsNHsd_3_batch11 | LEW.SsNHsd_2_batch11 | LEW.SsNHsd_1_batch11 | F344.NHsd_3_batch11 | F344.NHsd_2_batch11 | F344.NHsd_1_batch11 | SHR_2_batch1 | HXB7_2_batch1 | HXB7_1_batch1 | HXB27_2_batch1 | HXB27_1_batch1 | HXB25_2_batch1 | HXB25_1_batch1 | HXB2_2_batch1 | HXB2_1_batch1 | HXB17_2_batch1 | HXB17_1_batch1 | HXB13_2_batch1 | HXB13_1_batch1 | BXH12_2_batch1 | BXH12_1_batch1 | SHRSP_1_batch10 | LEW.Crl_1_batch10 | F344.NCl_1_batch10 | WKY_2_batch10 | WKY_1_batch10 | SS_1_batch11 | SHRSP_2_batch10 | LEW.Crl_2_batch10 | F344.NCl_2_batch10 | DA_2_batch10 | DA_1_batch10 | Cop.CrCrl_2_batch10 | ACI.SegHsd_2_batch10 | ACI.SegHsd_1_batch11 | HXB31_3_batch10 | HXB29_3_batch10 | BXH8_3_batch10 | BXH5_3_batch10 | BXH2_3_batch10 | LE.Stm_2_batch14 | BNLx_3_batch4 | LE.Stm_3_batch13 | F344.Stm_3_batch13 | F344.Stm_2_batch13 | F344.Stm_1_batch13 | SHR_1_batch6 | LE.Stm_1_batch14 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| PRN6.5G0000001 | 0.9015041 | 1.553993 | 2.381352 | 3.366840 | 1.621525 | 2.402869 | 2.389743 | 2.055506 | 2.789524 | 2.293886 | 2.035591 | 2.222622 | 1.264247 | 2.5615389 | 2.1922113 | 1.562573 | 1.199578 | 2.451458 | 2.382375 | 1.8580741 | 2.288696 | 2.6892576 | 0.8037906 | 2.713053 | 2.1153541 | 2.311140 | 1.9314869 | 2.704566 | 2.697639 | 1.937302 | 1.4867697 | 1.699251 | 1.967207 | 1.962481 | 2.510098 | 2.722358 | 1.925923 | 1.2435934 | 1.7463353 | 1.572330 | 2.190645 | 1.8098031 | 2.573240 | 1.6961145 | 1.287931 | 1.617457 | 2.662602 | 2.123104 | 0.7756686 | 2.864624 | 1.205841 | 1.243438 | 2.1043013 | 1.7271936 | 1.825702 | 1.9956577 | 2.7604304 | 2.0195789 | 3.2621524 | 1.257348 | 1.296388 | 1.311475 | 1.612577 | 3.0601113 | 2.4119596 | 1.587462 | 1.887902 | 1.9853786 | 2.567103 | 2.4493267 | 1.545996 | 2.1581425 | 2.2556750 | 2.517924 | 2.284219 | 2.237009 | 2.778412 | 2.213422 | 3.783119 | 3.054111 | 2.5732229 | 2.811710 | 2.276169 | 1.870567 | 1.8336147 | 1.824086 | 1.737258 | 2.3545748 | 1.289635 | 2.854276 | 2.023936 | 1.290977 | 2.285456 | 2.475756 | 2.751226 | 2.146168 | 2.5544311 | 3.145615 | 1.592265 | 1.829779 | 2.180615 | 1.325851 | 0.8801269 | 2.3431665 | 2.338004 | 1.7629701 | 2.5046370 | 1.771640 | 2.864588 | 1.955266 | 2.3402916 | 2.679990 | 0.8390833 | 0.8620538 | 1.590967 | 2.607304 | 2.762839 | 2.0859088 | 2.420274 | 1.7054236 | 1.313353 | 1.290057 | 1.958429 | 1.963241 | 2.799207 | 2.3981490 | 2.524465 | 2.158394 | 2.5467742 | 2.405483 | 1.8499461 | 2.747930 | 1.548196 | 1.580560 | 3.184267 |
| PRN6.5G0000002 | 4.5954611 | 4.590913 | 4.485530 | 5.185467 | 4.700294 | 4.214312 | 4.768959 | 4.657243 | 4.484925 | 4.088292 | 4.466700 | 3.933180 | 4.375247 | 4.4466475 | 3.3842843 | 4.088553 | 4.207381 | 4.567559 | 4.486802 | 4.3703531 | 4.265717 | 4.4979834 | 4.3902643 | 4.189746 | 4.2037329 | 4.353852 | 4.0866334 | 3.740454 | 4.128175 | 4.040205 | 4.2308143 | 4.362144 | 3.762126 | 4.277346 | 1.840842 | 3.573212 | 3.779802 | 4.2888660 | 3.8082694 | 3.501589 | 3.665834 | 4.3012751 | 3.743925 | 4.5077671 | 4.320372 | 4.048116 | 3.734434 | 4.512831 | 3.8069787 | 3.445512 | 4.591534 | 3.260750 | 4.5147919 | 4.4810237 | 4.506001 | 4.7509303 | 4.0866707 | 4.4005033 | 4.0101932 | 4.314301 | 4.611081 | 4.363652 | 4.040692 | 3.8958356 | 4.6485940 | 4.524782 | 4.254037 | 3.7097367 | 4.453297 | 3.8601061 | 3.801102 | 4.4805192 | 4.2243535 | 4.528530 | 4.076425 | 4.771581 | 3.737663 | 4.278753 | 1.964008 | 3.367746 | 4.0541765 | 4.719703 | 4.130910 | 4.110790 | 4.5990622 | 4.416181 | 3.925109 | 4.3133456 | 4.468875 | 4.050852 | 4.535176 | 4.679993 | 4.936068 | 4.767698 | 4.413069 | 4.504664 | 4.4381515 | 3.984339 | 4.398393 | 4.553390 | 4.130160 | 4.440855 | 4.3505861 | 3.5781595 | 5.450794 | 4.2818771 | 4.1727120 | 4.340343 | 4.659712 | 3.325563 | 4.4344559 | 3.751688 | 4.0235290 | 2.8982150 | 4.297711 | 4.173370 | 4.437450 | 4.3443649 | 4.179917 | 4.4770655 | 4.139544 | 3.817244 | 3.750947 | 3.681832 | 4.519668 | 3.4900481 | 4.432348 | 4.258772 | 3.9009047 | 4.217468 | 4.7358738 | 4.496875 | 4.230501 | 4.379841 | 4.145373 |
| PRN6.5G0000003 | 1.4271851 | 1.579125 | 1.617124 | 2.094803 | 1.391773 | 1.634894 | 1.043924 | 1.366452 | 1.060712 | 2.708008 | 2.147084 | 2.721420 | 1.029104 | 1.6520845 | 2.5947245 | 1.588224 | 2.051738 | 1.770452 | 1.617969 | 0.6152209 | 1.409059 | 1.3190398 | 1.7295608 | 2.398055 | 0.5570825 | 0.995394 | 0.5515705 | 1.966052 | 1.783593 | 1.719163 | 0.5499458 | 2.357587 | 1.543104 | 2.323452 | 1.515368 | 1.273791 | 1.708155 | 1.0099135 | 0.5593437 | 1.807811 | 2.125097 | 2.4937162 | 2.629711 | 0.5341352 | 2.181431 | 1.387901 | 2.447314 | 1.732042 | 1.6790040 | 1.307649 | 1.735882 | 1.009769 | 2.3591144 | 0.5497403 | 1.348221 | 1.9516416 | 2.0799091 | 1.7988076 | 0.6083105 | 1.595660 | 1.856924 | 2.058692 | 1.383256 | 1.3800773 | 1.0576368 | 1.825094 | 1.401889 | 1.5594447 | 2.051381 | 1.3123192 | 1.777746 | 0.5761805 | 1.6417638 | 2.298888 | 1.075442 | 2.016431 | 1.380298 | 1.351208 | 2.221713 | 2.247345 | 1.5646468 | 1.663550 | 1.873219 | 2.333388 | 0.6030221 | 1.810047 | 1.517164 | 0.5953389 | 1.635799 | 2.096441 | 2.392712 | 1.379828 | 1.881795 | 1.695129 | 1.540888 | 2.080052 | 1.3878175 | 1.917657 | 2.009587 | 1.994150 | 1.009052 | 1.418752 | 1.0663993 | 2.1246021 | 0.588233 | 0.5676835 | 2.1492623 | 1.755749 | 1.921475 | 1.460038 | 2.1217973 | 2.041854 | 1.3328068 | 2.3068599 | 1.362693 | 0.643840 | 2.115537 | 2.4625374 | 1.538913 | 0.6701127 | 2.218834 | 0.616753 | 2.198903 | 1.539539 | 0.957446 | 0.5569069 | 2.054794 | 1.764562 | 0.9840184 | 1.849229 | 2.0161829 | 3.123833 | 2.366216 | 1.031403 | 1.669373 |
phenoGenMarkerSets=getMarkerSets()
| marker_set_id | display_name | organism | genome_version | panel | description | type |
|---|---|---|---|---|---|---|
| 1 | HRDPv6 Markers | Rat | rn7.2 | HRDP | HRDP v6 markers from strain sequencing variant calls | Marker |
| 2 | HRDPv4 Markers | Rat | rn6 | HRDP | STAR Consortium Genotype Arrays ( http://oct2012.archive.ensembl.org/Rattus_norvegicus/Info/Content?file=star.html ) | Marker |
| 3 | HXB/BXH Markers | Rat | rn5 | HXB/BXH | STAR Consortium Genotype Arrays ( http://oct2012.archive.ensembl.org/Rattus_norvegicus/Info/Content?file=star.html ) | Marker |
| 4 | BXD Markers | Mouse | mm9 | BXD | Wellcome-CTC Mouse Strain SNP Genotype Set | Marker |
| 5 | LXS Markers | Mouse | mm10 | LXS | Affymetrix Mouse Diversity SNP Array | Marker |
2. Get a list of marker files linked to the selected marker set by providing the marker_set_id from step 1.
phenoGenMarkerFiles=getMarkerFiles(markerSetID=1)
| download_file_id | marker_set_id | description | filename | checksum | URL |
|---|---|---|---|---|---|
| 1 | 1 | HRDPv6 Marker Genotypes | HRDP.v6.rn7.genotypes.2023-01-17.txt.gz | 110da4cb07901b7e8fcec0778d89a141 | https://phenogen.org/web/sysbio/downloadLink.jsp?url=/downloads/Markers/HRDP.v6.rn7.genotypes.2023-01-17.txt.gz |
| 2 | 1 | HRDPv6 Marker Positions | HRDP.v6.rn7.positions.2023-01-17.txt.gz | 22e76bcdb6a8b4aa6cf75ea73f969bd1 | https://phenogen.org/web/sysbio/downloadLink.jsp?url=/downloads/Markers/HRDP.v6.rn7.positions.2023-01-17.txt.gz |
3. Get a dataframe with the data from a selected file. Provide the URL from step 2 to specify the file to load.
phenogenMarkerData=getMarkerFile(URL="https://phenogen.org/web/sysbio/downloadLink.jsp?url=/downloads/Markers/HRDP.v6.rn7.genotypes.2023-01-17.txt.gz")
| BN.Lx_Cub_mRatNor1 | BXH10_mRatNor1 | BXH11_mRatNor1 | BXH12_mRatNor1 | BXH13_mRatNor1 | BXH2_mRatNor1 | BXH3_mRatNor1 | BXH5_mRatNor1 | BXH6_mRatNor1 | BXH8_mRatNor1 | BXH9_mRatNor1 | HXB1_mRatNor1 | HXB10_mRatNor1 | HXB13_mRatNor1 | HXB15_mRatNor1 | HXB17_mRatNor1 | HXB18_mRatNor1 | HXB2_mRatNor1 | HXB20_mRatNor1 | HXB21_mRatNor1 | HXB22_mRatNor1 | HXB23_mRatNor1 | HXB24_mRatNor1 | HXB25_mRatNor1 | HXB27_mRatNor1 | HXB29_mRatNor1 | HXB3_mRatNor1 | HXB31_mRatNor1 | HXB4_mRatNor1 | HXB5_mRatNor1 | HXB7_mRatNor1 | SHR_OlaIpcv_mRatNor1 | ACI_EurMcwi_2019NOV | BN_NHsdMcwi_2019 | BUF_N_2020 | DA_OlaHsd_2019NOV | F344_NCrl_2019NOV | F344_NHsd_2021 | F344_Stm_2019 | FHH_EurMcwi_2019NOV | FXLE12_Stm_2019NOV | FXLE13_Stm_2019NOV | FXLE14_Stm_2019NOV | FXLE15_Stm_2019NOV | FXLE16_Stm_2019 | FXLE17_Stm_2019NOV | FXLE18_Stm_2019 | FXLE20_Stm_2019NOV | GK_FarMcwi_2019NOV | LE_Stm_2019 | LEW_Crl_2019 | LXF10A_StmMcwi_2020 | LEXF11_Stm_2020 | LEXF1A_Stm_2019 | LEXF1C_Stm_2019 | LEXF2B_Stm_2019 | LEXF3_Stm_2020 | LEXF4_Stm_2020 | LEXF5_Stm_2019NOV | LEXF6B_Stm_2019NOV | LEXF6B_Stm_2021_A | LEXF6B_Stm_2021_BH | LEXF6B_Stm_2021_FH | LEXF7A_Stm_2019NOV | LEXF8A_Stm_2021 | LH_MavRrrcAek_2020 | LL_MavRrrcAek_2020 | LN_MavRrrcAek_2020 | M520_N_2020 | MR_N_2020 | MWF_Hsd_2019NOV | PVG_Seac_2019 | RCS_LavRrrc_2021 | SHR_NCrl_2021 | SHRSP_A3NCrl_2019NOV | SR_JrHsd_2020 | SS_JrHsd_2021 | WAG_RijCrl_2020 | WKY_N_2020 | WKY_NCrl_2019 | WN_N_2020 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| chr1_16211 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 2 | 2 | 0 | 2 | 0 | 2 | 2 | 0 | 2 | 0 | 2 | 0 | 0 | 0 | 2 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| chr1_17226 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 2 | 2 | 0 | 2 | 0 | 2 | 2 | 0 | 2 | 0 | 2 | 0 | 0 | 0 | 2 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| chr1_17294 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 2 | 2 | 0 | 2 | 0 | 2 | 2 | 0 | 2 | 0 | 2 | 0 | 0 | 0 | 2 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
https://github.com/TabakoffLab/PhenoGenRESTAPI
https://rest-doc.phenogen.org - Documentation of current functions. Please note some may be under development. Future updates will seperate development and production documentation.
All functions should include help as a response if you call the function
with this appended to the end ?help=Y. The response returns a JSON
object with supported methods and then list of parameters and
description of each parameter as well as a list of options if there is a
defined list of values.