Single-sample GSEA transformation
Arguments
- mat
A numeric matrix.
- gs
A list of gene sets. Genes should have the same ID type as in
mat.- scale
Whether to apply z-score scaling on rows?
- set_level
A function to calculate the geneset-level score. This function should accept two arguments: a vector of scores for all genes, and a corresponding logical vector repressenting which genes are in the current gene set.
Examples
data(p53_dataset)
expr = p53_dataset$expr
gs = p53_dataset$gs
mat_gs = ss_gsea(expr, gs)
head(mat_gs)
#> X786.0 BT.549 CCRF.CEM COLO.205 EKVX
#> 41bbPathway 0.5721238 0.3716575 -0.03419229 -0.3803926 -0.17893732
#> ace2Pathway 0.1150494 -0.1215859 -0.53927782 -0.5206118 0.07957701
#> acetaminophenPathway 0.7119185 -0.7219183 -0.24630432 -0.4053178 -0.06886475
#> achPathway 0.1695001 0.0124123 0.50325172 -0.2961399 -0.33026951
#> actinYPathway -0.5898666 0.1509440 0.09254110 -0.6550168 -0.29620835
#> agpcrPathway 0.3056068 -0.3469833 0.22963846 -0.4034337 0.07078834
#> HCC.2998 HCT.15 HOP.62 HOP.92
#> 41bbPathway 0.10626012 -0.01356768 0.37492685 -0.11419128
#> ace2Pathway -0.06029373 -0.45067546 0.19145159 0.18684321
#> acetaminophenPathway -0.31668970 -0.31598656 0.39354926 -0.40100280
#> achPathway -0.28396887 -0.04807015 -0.27747298 -0.44336771
#> actinYPathway 0.12333378 -0.23761987 0.05979451 0.22101402
#> agpcrPathway -0.67816740 -0.53734152 0.04512116 -0.07729705
#> HS.578T HT29 K.562 KM12
#> 41bbPathway -0.04994074 -0.18924036 -0.005963629 -0.20893435
#> ace2Pathway 1.14660761 -0.06168806 -0.216575126 -0.36083639
#> acetaminophenPathway 0.53864238 -0.52610568 0.309069060 -0.01298177
#> achPathway -0.05929257 0.18103222 -0.335725023 -0.27550963
#> actinYPathway 0.25260140 -0.05067002 -0.359799705 0.35064838
#> agpcrPathway -0.29671158 -0.57691305 0.750348698 -0.47843059
#> M14 MDA.MB.231.ATCC MDA.MB.435 NCI.H23
#> 41bbPathway -0.1884429 0.07285171 -0.20801352 -0.1040037
#> ace2Pathway -0.1363734 -0.34398995 -0.24756707 -0.3974075
#> acetaminophenPathway -0.5185060 -0.57863908 -0.09553902 0.4852677
#> achPathway -0.3207411 0.04745092 0.19951061 -0.2217484
#> actinYPathway 0.5578817 0.04598913 0.21846789 0.2022725
#> agpcrPathway 0.1183200 -0.09693392 -0.09628469 0.3306239
#> NCI.H322M NCI.H522 OVCAR.3 OVCAR.5 OVCAR.8
#> 41bbPathway 0.26486231 0.33999053 0.2623441 0.03621417 -0.1222128
#> ace2Pathway -0.08871991 -0.61364549 0.3953051 0.05046776 -0.2256692
#> acetaminophenPathway 0.24843338 -0.52213915 0.3826191 -0.25680728 -0.2318977
#> achPathway 0.56894615 -0.08125878 0.6331867 0.10085314 0.2978465
#> actinYPathway -0.07839660 0.32193300 -0.0484540 -0.38456584 -0.2461460
#> agpcrPathway -0.10183342 0.46315505 0.1904777 -0.22047566 -0.1482666
#> PC.3 RXF.393 SF.268 SF.295
#> 41bbPathway -0.367647540 0.70307461 0.13816271 0.08380162
#> ace2Pathway -0.549911229 -0.03108937 0.20299944 -0.35823572
#> acetaminophenPathway -0.096277074 0.97222403 -0.04890103 -0.29169099
#> achPathway 0.006470029 0.04851479 0.21356620 -0.24726560
#> actinYPathway -0.313699115 -0.06042797 -0.05364847 -0.02145482
#> agpcrPathway -0.162792092 0.28068162 0.74907910 -0.12161759
#> SK.MEL.2 SN12C SNB.19 SNB.75 SW.620
#> 41bbPathway 0.2198677 -0.2459852 -0.1428077 -0.06085097 -0.21290326
#> ace2Pathway -0.5088797 -0.4270613 0.2079099 0.43510540 -0.47359220
#> acetaminophenPathway -0.5159262 0.4583862 1.0251767 -0.30382062 -0.33630877
#> achPathway -0.1259368 0.4694338 -0.1092592 0.10332531 -0.07836556
#> actinYPathway 0.4424018 0.0198115 -0.1912613 0.17624852 -0.30873648
#> agpcrPathway 0.0955258 0.3665543 0.2771834 -0.24934697 -0.28255251
#> T.47D U251 A498 A549.ATCC ACHN
#> 41bbPathway -0.35350932 -0.33010142 0.44530267 -0.1580738 -0.05169276
#> ace2Pathway -0.35987801 0.22097953 0.46689204 0.7314822 0.47436482
#> acetaminophenPathway -0.56042375 0.21693683 0.37951156 0.5488031 -0.73347586
#> achPathway -0.04505649 -0.16812274 -0.05785023 -0.1192585 -0.01661068
#> actinYPathway -0.42982226 0.03434598 0.17498022 -0.3036893 0.26605746
#> agpcrPathway -0.35743853 0.43198789 -0.05491016 -0.4415421 -0.27916591
#> CAKI.1 HCT.116 LOX.IMVI MALME.3M
#> 41bbPathway -0.244779899 -0.1006201 0.33764334 -0.08916169
#> ace2Pathway 0.008909841 -0.4487473 -0.23490020 -0.09868361
#> acetaminophenPathway -0.113470566 -1.0274496 0.02708292 -0.01892766
#> achPathway -0.094527508 -0.3372435 -0.10600546 0.06179853
#> actinYPathway -0.156996859 -0.2556593 0.27260077 0.37517476
#> agpcrPathway 0.034521276 -0.2521381 -0.33699830 0.20072880
#> MCF7 MOLT.4 NCI.H460 OVCAR.4 SF.539
#> 41bbPathway -0.11747436 0.4444458 0.06408283 -0.02384906 -0.13952795
#> ace2Pathway 0.11933998 -0.2080729 0.85966316 0.39370032 0.64369124
#> acetaminophenPathway -0.22222806 0.5773385 0.83322594 1.61148209 -0.43261073
#> achPathway 0.18913955 0.2068222 -0.40095440 0.31791504 -0.16697275
#> actinYPathway -0.09374744 -0.2153535 -0.10847776 -0.07891680 -0.03325021
#> agpcrPathway 0.08859516 0.3560098 0.36606696 -0.48187246 0.26640656
#> SK.MEL.5 SR UACC.257 UACC.62 UO.31
#> 41bbPathway 0.1968299 0.016528468 -0.50217533 -0.25179350 0.14001610
#> ace2Pathway 0.5741174 0.147216325 -0.28103333 0.03288648 0.68044168
#> acetaminophenPathway 0.5914818 -0.102059842 -0.12046868 0.33260513 -0.50101511
#> achPathway 0.1032344 0.417725038 0.01113510 0.29147789 -0.10755418
#> actinYPathway 0.5589044 0.186858322 -0.01078968 0.23435538 0.24351468
#> agpcrPathway 0.6122329 0.009465496 0.32885093 0.17773933 -0.06626231