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MSKCC-Epi-Bio / gnomeR

Package to wrangle and visualize genomic data in R
https://mskcc-epi-bio.github.io/gnomeR/
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Pathways bug #315

Closed karissawhiting closed 1 year ago

karissawhiting commented 1 year ago

is pathway doing and not or?!

kit_sum<- kit_gen %>% select(-all_of(clin_vars)) %>% summarize_by_gene() %>% add_pathways(pathways = NULL, custom_pathways = c("CDKN2A.any", "CDKN2B.any"))

Characteristic N = 3141
KIT 309 (98%)
KIT Exon 11 261 (83%)
CDKN2A 92 (29%)
pathway_custom...135 77 (25%)
CDKN2B 77 (25%)
pathway_custom...166 77 (25%)
KIT Exon 9 35 (11%)
RB1 25 (8.0%)
MGA 18 (5.7%)
SETD2 17 (5.4%)
TP53 16 (5.1%)
MAX 15 (4.8%)
TNFRSF14 12 (3.8%)
PTEN 11 (3.5%)
GATA3 10 (3.2%)
Primary KIT Exon 13/14 10 (3.2%)
TERT 9 (2.9%)
TSC1 9 (2.9%)
PIK3CA 8 (2.5%)
PDGFRA 8 (2.5%)
Primary KIT Exon 17/18 7 (2.2%)
CDKN2C 6 (1.9%)
FOXA1 6 (1.9%)
NFKBIA 6 (1.9%)
CCNE1 6 (1.9%)
PAX5 5 (1.6%)
RICTOR 5 (1.6%)
ARID1A 5 (1.6%)
KMT2D 5 (1.6%)
ID3 4 (1.3%)
KDR 4 (1.3%)
AKT2 4 (1.3%)
ARID1B 4 (1.3%)
DNMT3A 4 (1.3%)
FBXW7 3 (1.0%)
KMT2C 3 (1.0%)
PIK3R1 3 (1.0%)
NOTCH1 3 (1.0%)
EPHA7 3 (1.0%)
MCL1 3 (1.0%)
FGFR4 3 (1.0%)
FGF4 3 (1.0%)
FGF3 3 (1.0%)
FGF19 3 (1.0%)
ATM 3 (1.0%)
NF1 3 (1.0%)
RBM10 3 (1.0%)
RAD50 2 (0.6%)
CBL 2 (0.6%)
KRAS 2 (0.6%)
CCNQ 2 (0.6%)
RTEL1 2 (0.6%)
B2M 2 (0.6%)
BLM 2 (0.6%)
PRDM1 2 (0.6%)
RAD51B 2 (0.6%)
RAD51 2 (0.6%)
SMARCB1 2 (0.6%)
TP53BP1 2 (0.6%)
IKZF1 2 (0.6%)
CCND1 2 (0.6%)
ETV1 2 (0.6%)
MDM2 2 (0.6%)
PPM1D 2 (0.6%)
MYC 2 (0.6%)
ANKRD11 2 (0.6%)
ATR 2 (0.6%)
EP300 2 (0.6%)
FGFR1 2 (0.6%)
KMT2A 2 (0.6%)
NF2 2 (0.6%)
RECQL 2 (0.6%)
PTPRS 1 (0.3%)
MSH2 1 (0.3%)
PTPRD 1 (0.3%)
KMT2B 1 (0.3%)
ERBB4 1 (0.3%)
MTOR 1 (0.3%)
BAP1 1 (0.3%)
NCOR1 1 (0.3%)
MED12 1 (0.3%)
LATS1 1 (0.3%)
MSH6 1 (0.3%)
RET 1 (0.3%)
CREBBP 1 (0.3%)
EGFR 1 (0.3%)
ASXL1 1 (0.3%)
PPP2R1A 1 (0.3%)
MEN1 1 (0.3%)
CTCF 1 (0.3%)
CLCN5 1 (0.3%)
SMAD4 1 (0.3%)
NLRP6 1 (0.3%)
PHOX2B 1 (0.3%)
C11orf65 1 (0.3%)
JAK2 1 (0.3%)
NTRK3 1 (0.3%)
ERRFI1 1 (0.3%)
STK11 1 (0.3%)
PMAIP1 1 (0.3%)
SESN1 1 (0.3%)
SESN2 1 (0.3%)
KLF4 1 (0.3%)
SPRED1 1 (0.3%)
TCF3 1 (0.3%)
FANCC 1 (0.3%)
PRKN 1 (0.3%)
CHEK2 1 (0.3%)
PALB2 1 (0.3%)
ERCC4 1 (0.3%)
WT1 1 (0.3%)
SOCS1 1 (0.3%)
FAT1 1 (0.3%)
HLA-B 1 (0.3%)
AMER1 1 (0.3%)
GRIN2A 1 (0.3%)
MUTYH 1 (0.3%)
TP63 1 (0.3%)
DICER1 1 (0.3%)
ZRSR2 1 (0.3%)
CCND3 1 (0.3%)
CCND2 1 (0.3%)
YAP1 1 (0.3%)
IKBKE 1 (0.3%)
PAK1 1 (0.3%)
MYCN 1 (0.3%)
AXL 1 (0.3%)
MDM4 1 (0.3%)
DDR2 1 (0.3%)
AKT3 1 (0.3%)
KDM5A 1 (0.3%)
PIK3R2 1 (0.3%)
AGO2 1 (0.3%)
MAPK1 1 (0.3%)
MYCL 1 (0.3%)
GLI1 1 (0.3%)
KIT Other 1 (0.3%)
BCOR 1 (0.3%)
RAC1 1 (0.3%)
SDHA 1 (0.3%)
AKT1 0 (0%)
BMPR1A 0 (0%)
BRAF 0 (0%)
ESR1 0 (0%)
FOXP1 0 (0%)
NOTCH2 0 (0%)
ABHD3 0 (0%)
FANCA 0 (0%)
TSC2 0 (0%)
FOXO1 0 (0%)
SUZ12 0 (0%)
RAD51D 0 (0%)
SPEN 0 (0%)
CDK4 0 (0%)
CARD11 0 (0%)
BRD4 0 (0%)
YES1 0 (0%)
NF1 Deficient 0 (0%)
PDGFRA D842V 0 (0%)
SDH Deficient 0 (0%)
Unknown 0 (0%)
PDGFRA Other 0 (0%)
BRAF V600E 0 (0%)
WT 0 (0%)
SDHB 0 (0%)

1 n (%)