Is GTEx age and sex data available via the recount package?
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Entering edit mode
abe • 0
@abe-18006
Last seen 2.0 years ago

Apologies for such a simple question. I’m able to locate age and sex data for TCGA data via the recount package, but I’m having trouble finding the same data for GTEx.

> download_study("SRP012682", type = "rse-gene")

> load(file.path("SRP012682", "rse_gene.Rdata"))

> colnames(colData(rse_gene))

[1] "project"

[2] "sample"

[3] "experiment"

[4] "run"

[5] "read_count_as_reported_by_sra"

[6] "reads_downloaded"

[7] "proportion_of_reads_reported_by_sra_downloaded"

[8] "paired_end"

[9] "sra_misreported_paired_end"

[10] "mapped_read_count"

[11] "auc"

[12] "sharq_beta_tissue"

[13] "sharq_beta_cell_type"

[14] "biosample_submission_date"

[15] "biosample_publication_date"

[16] "biosample_update_date"

[17] "avg_read_length"

[18] "geo_accession"

[19] "bigwig_file"

[20] "sampid"

[21] "smatsscr"

[22] "smcenter"

[23] "smpthnts"

[24] "smrin"

[25] "smts"

[26] "smtsd"

[27] "smubrid"

[28] "smtspax"

[29] "smtstptref"

[30] "smnabtch"

[31] "smnabtcht"

[32] "smnabtchd"

[33] "smgebtch"

[34] "smafrze"

[35] "smgtc"

[36] "sme2mprt"

[37] "smchmprs"

[38] "smntrart"

[39] "smnumgps"

[40] "smmaprt"

[41] "smexncrt"

[42] "sm550nrm"

[43] "smgnsdtc"

[44] "smunmprt"

[45] "sm350nrm"

[46] "smrdlgth"

[47] "smmncpb"

[48] "sme1mmrt"

[49] "smsflgth"

[50] "smestlbs"

[51] "smmppd"

[52] "smnterrt"

[53] "smrrnanm"

[54] "smrdttl"

[55] "smvqcfl"

[56] "smmncv"

[57] "smtrscpt"

[58] "smmppdpr"

[59] "smcglgth"

[60] "smgappct"

[61] "smunpdrd"

[62] "smntrnrt"

[63] "smmpunrt"

[64] "smexpeff"

[65] "smmppdun"

[66] "sme2mmrt"

[67] "sme2anti"

[68] "smaltalg"

[69] "sme2snse"

[70] "smmflgth"

[71] "sme1anti"

[72] "smspltrd"

[73] "smbsmmrt"

[74] "sme1snse"

[75] "sme1pcts"

[76] "smrrnart"

[77] "sme1mprt"

[78] "smnum5cd"

[79] "smdpmprt"

[80] "sme2pcts"

[81] "title"

[82] "characteristics"


# Search for sex data

> which(as.data.frame(colData(rse_gene))=="Male", arr.ind=TRUE)

    row col

# Double-check for additional metadata

> rse_gene

class: RangedSummarizedExperiment

dim: 58037 9662

metadata(0):

assays(1): counts

rownames(58037): ENSG00000000003.14 ENSG00000000005.5 ...

  ENSG00000283698.1 ENSG00000283699.1

rowData names(3): gene_id bp_length symbol

colnames(9662): SRR660824 SRR2166176 ... SRR612239 SRR615898

colData names(82): project sample ... title characteristics
recount gtex • 1.3k views
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Entering edit mode
@lcolladotor
Last seen 12 days ago
United States

Hi @abe,

Under the metadata section in https://f1000research.com/articles/6-1558/v1 we state that " we compiled metadata for GTEx using the v6 phenotype information available at gtexportal.org". This was also mentioned in the supplementary material of the recount2 paper https://www.nature.com/articles/nbt.3838#supplementary-information https://media.nature.com/original/nature-assets/nbt/journal/v35/n4/extref/nbt.3838-S1.pdf  "For GTEx we included the metadata from the file “GTEx Data V6 Annotations SampleAttributesDS.txt” available from http://www.gtexportal.org/home/datasets." Similarly, if you load the recount Bioconductor package and look at the help file for "all_metadata" you'll see: "Note that for subset = 'gtex', there are more variables than the ones we have for 'sra'. This information corresponds to file GTEx_Data_V6_Annotations_SampleAttributesDS.txt available at http://www.gtexportal.org/home/datasets. There you can find the information describing these variables."

If you go to the GTEx portal you can find a data dictionary for the variables. See https://imgur.com/a/sixZeNk The file you want to look at is called "GTEx_Data_V6_Annotations_SampleAttributesDD.xlsx". You can use the information from "sampid" to find the subject id and match it with the GTEx v6 subject annotation table "GTEx_Data_V6_Annotations_SubjectPhenotypesDS.txt" (also from the GTEx portal) https://storage.googleapis.com/gtex_analysis_v6p/annotations/GTEx_Data_V6_Annotations_SubjectPhenotypesDS.txt that has the sex and age information.

Best,

Leonardo

 

 

 

 

 

 

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