Pathways bug
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karissawhiting commented
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 (%) |