I have the following data frame:
> str(Long_top)
'data.frame': 110 obs. of 6 variables:
$ Category : chr "GOTERM_BP_DIRECT" "GOTERM_CC_DIRECT" "GOTERM_MF_DIRECT" "GOTERM_CC_DIRECT" ...
$ Term : chr "GO:0016579~protein deubiquitination" "GO:0005634~nucleus" "GO:0004843~thiol-dependent ubiquitin-specific protease activity" "GO:0005654~nucleoplasm" ...
$ Count : int 13 57 12 43 21 14 11 7 18 14 ...
$ Genes : chr "8287, 64854, 373509, 5071, 55031, 80124, 57646, 126119, 84132, 85015, 159195, 84640, 56957" "9785, 10293, 9425, 6872, 8335, 122402, 80124, 11107, 10419, 54476, 6667, 85015, 10013, 84640, 55206, 5976, 5934"| __truncated__ "80124, 57646, 126119, 8287, 64854, 373509, 84132, 85015, 159195, 84640, 55031, 56957" "9785, 6872, 10293, 4298, 8315, 22992, 11107, 57646, 10419, 79039, 23186, 54531, 54476, 6601, 6667, 11342, 54856"| __truncated__ ...
$ Fold.Enrichment: num 26.34 2.24 21.31 2.54 5.08 ...
$ Benjamini : num 4.05e-11 1.21e-09 1.61e-09 7.00e-08 2.50e-07 ...
I want to subtract all the rows when the number "56957" appears in the Genes column. I add here several rows from my file so if someone wants to practice writen code to validate it works:)
Thank you!
Category Term Count % PValue Genes List Total Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini FDR
GOTERM_BP_DIRECT GO:0016579~protein deubiquitination 13 14.444444444444443 6.470567352790495E-14 8287, 64854, 373509, 5071, 55031, 80124, 57646, 126119, 84132, 85015, 159195, 84640, 56957 88 108 19256 26.33922558922559 4.0583203464450435E-11 4.0505751628468494E-11 3.972928354613364E-11
GOTERM_CC_DIRECT GO:0005634~nucleus 57 63.33333333333333 7.536809948339279E-12 9785, 10293, 9425, 6872, 8335, 122402, 80124, 11107, 10419, 54476, 6667, 85015, 10013, 84640, 55206, 5976, 5934, 9618, 6047, 64324, 23410, 3010, 5071, 56980, 83860, 4857, 4858, 4674, 64854, 1482, 85509, 57646, 79039, 23186, 54531, 11166, 29081, 54856, 6602, 6604, 56957, 5451, 8287, 6663, 55031, 221613, 8481, 27030, 5928, 57332, 9924, 11011, 84132, 54107, 84333, 8438, 140628 88 5930 20472 2.2361336808217076 1.2134344640202244E-9 1.213426401682624E-9 1.1606687320442489E-9
GOTERM_MF_DIRECT GO:0004843~thiol-dependent ubiquitin-specific protease activity 12 13.333333333333334 8.618779898787077E-12 80124, 57646, 126119, 8287, 64854, 373509, 84132, 85015, 159195, 84640, 55031, 56957 89 119 18811 21.313568123878763 1.6030916594189648E-9 1.6117118410731834E-9 1.4824301425913772E-9
GOTERM_CC_DIRECT GO:0005654~nucleoplasm 43 47.77777777777778 8.689750582410526E-10 9785, 6872, 10293, 4298, 8315, 22992, 11107, 57646, 10419, 79039, 23186, 54531, 54476, 6601, 6667, 11342, 54856, 85015, 10013, 6602, 5976, 6604, 5934, 9618, 4261, 9972, 5451, 6663, 6047, 93426, 64324, 23410, 55031, 27030, 5928, 57332, 84132, 83860, 54107, 84333, 8438, 4857, 140628 88 3939 20472 2.5395693415495395 1.399049657235807E-7 6.995249218840473E-8 6.691107948456104E-8
GOTERM_MF_DIRECT GO:0008270~zinc ion binding 21 23.333333333333332 2.670087630679821E-9 23409, 6047, 10193, 8315, 64324, 131405, 22992, 23410, 5192, 5071, 286827, 80128, 57159, 142678, 85015, 10013, 54469, 5976, 9618, 56957, 140628 89 873 18811 5.084250357156646 4.966361700775579E-7 2.496531934685633E-7 2.296275362384646E-7
GOTERM_MF_DIRECT GO:0061630~ubiquitin protein ligase activity 14 15.555555555555555 4.03154249513981E-9 10293, 10193, 8315, 55072, 131405, 5071, 286827, 57630, 57159, 54476, 7844, 11342, 344558, 142678 89 328 18811 9.021444231296245 7.498666335647997E-7 2.512994821970482E-7 2.3114176972134912E-7
GOTERM_BP_DIRECT GO:0006511~ubiquitin-dependent protein catabolic process 11 12.222222222222221 5.735417980008066E-7 57646, 8287, 6872, 64854, 11342, 373509, 84132, 85015, 84640, 55031, 5071 88 282 19256 8.535460992907801 3.5954615828870384E-4 1.7951858277425245E-4 1.7607733198624762E-4
GOTERM_BP_DIRECT GO:0051865~protein autoubiquitination 7 7.777777777777778 1.2120304473656288E-6 6047, 10193, 57630, 11342, 344558, 131405, 5071 88 76 19256 20.154306220095695 7.596548670514292E-4 2.529103533502945E-4 2.48062231560832E-4
Thanks in advance!
