From the link https://gtexportal.org/home/datasets, under V7, I'm trying to do R/Python analyses on the Gene TPM and Transcript TPM files. But in these files (and to open them I had to use Universal Viewer since the files are too large to view with an app like NotePad), I'm seeing a bunch of ID's for samples (i.e. GTEX-1117F-0226-SM-5GZZ7
), followed by transcript ID's like ENSG00000223972.4, and then a bunch of numbers like 0.02865 (and they take up like 99% of the large files). Can someone help me decipher what the numbers mean, please? And are the numbers supposed to be assigned to a specific sample ID? (The amount of letters far exceed the amount of samples, btw). I tried opening these files as tables in R but I do not think R is categorizing the contents of the file correctly.
For context, I am planning to match males with females for sex comparison but in order to do that, I need to get R to categorize everything correctly. (I know that females have "F" where ####-#####-####-#x-#####
where x
is and males have "M").
Example subsets
For gene TPM:
#1.2 56202 11688
Name Description GTEX-1117F-0226-SM-5GZZ7 GTEX-111CU-1826-SM-5GZYN GTEX-111FC-0226-SM-5N9B8 GTEX-111VG-2326-SM-5N9BK GTEX-111YS-2426-SM-5GZZQ GTEX-1122O-2026-SM-5NQ91 GTEX-1128S-2126-SM-5H12U GTEX-113IC-0226-SM-5HL5C 7C-0005-SM-57WDL GTEX-ZVE2-0006-SM-51MRW GTEX-ZVZQ-0006-SM-51MR8 GTEX-ZXES-0005-SM-57WCB GTEX-ZXG5-0005-SM-57WCN
ENSG00000223972.4 DDX11L1 0.1082 0.1158 0.02104 0.02329 0 0.04641 0.03076 0.09358 0.121 0.02859 0 0.02373 0.08024 0.02231 0.0189 0.09309 0.07772 0.1596 0.1173 0.07969 0.07763 0.02062 0.07831 0.05159 0.1181 0.04187
For transcript TPM:
transcript_id gene_id GTEX-1117F-0226-SM-5GZZ7 GTEX-1117F-0426-SM-5EGHI GTEX-1117F-0526-SM-5EGHJ GTEX-1117F-0626-SM-5N9CS GTEX-1117F-0726-SM-5GIEN GTEX-1117F-1326-SM-5EGHH GTEX-1117F-2226-SM-5N9CH GTEX-1117F-2426-SM-5EGGH GTEX-111CU-0226-SM-5GZXC GTEX-111CU-0326-SM-5GZXO
ENST00000373020.4 ENSG00000000003.10 26.84 4.13 13.54 31.17 6.87 39.75 32.25 30.81 19.69 46.42 9.07 27.83 9.04 12.87 18.18 11.12 11.28 7.86 5.52 24.67 6.48 8.13 21.41 5.39 7.98 8.56 51.61 12.51 70.01 17.48 2.1 14.16 3.96 11.39 1.29 6.5 29.93 4.74 3.1 20.82 16.81 14.82 50.8 16.9 9.35 39.3 3.61 2.87 11.73