custom_pathway \ Enables creation of a custom pathway binary matrix from a binmat() object. Similarly to the internal file 'pathways.csv', this function takes as input a data frame containing the name of the pathways of interest, and for each pathways a character vector of the genes of interest. Note that the different events to be considered in each pathways must be considered separetely. For example, if one wishes to consider TP53 deletions in a given pathway, one must specify "TP53.Del" in the character vector for that pathway.

custom_pathway(mat, pathway)

Arguments

mat

a binmat() binary matrix

pathway

a dataframe/tibble with first column the name of the genes, and second column their corresponding pathway

Value

pathway_dat : a binary matrix of pathway level alterations

Examples

library(gnomeR) patients <- as.character(unique(mut$Tumor_Sample_Barcode))[1:200] bin.mut <- binmat(patients = patients,maf = mut)
#> Warning: MUTATION DATA: To ensure gene with multiple names/aliases are correctly grouped together, the #> following genes in your maf dataframe have been recoded. You can supress this with recode.aliases = FALSE #> #> AMER1 recoded to FAM123B
#> Warning: All samples were sequenced on the same platform. #> The specify.plat argument has been overwritten to FALSE.
pathway <- as.data.frame(cbind(c("path1","path1","path2","path3"),c("PIK3CA","KRAS","TERT","TP53"))) custom_pathway(mat = bin.mut, pathway = pathway)
#> path1 path2 path3 #> P-0000062-T01-IM3 0 0 1 #> P-0000065-T01-IM3 0 1 0 #> P-0000113-T01-IM3 0 0 1 #> P-0000140-T01-IM3 0 0 0 #> P-0000145-T01-IM3 1 0 1 #> P-0000157-T01-IM3 1 0 0 #> P-0000185-T01-IM3 0 0 1 #> P-0000088-T01-IM3 0 1 1 #> P-0000193-T01-IM3 0 0 0 #> P-0000230-T01-IM3 1 0 1 #> P-0000231-T01-IM3 0 0 1 #> P-0000242-T01-IM3 0 0 1 #> P-0000244-T01-IM3 0 0 1 #> P-0000270-T01-IM3 0 0 1 #> P-0000281-T01-IM3 0 0 0 #> P-0000300-T01-IM3 0 0 0 #> P-0000329-T01-IM3 0 0 1 #> P-0000336-T01-IM3 0 1 1 #> P-0000340-T01-IM3 0 0 0 #> P-0000363-T01-IM3 0 0 1 #> P-0000370-T01-IM3 0 0 1 #> P-0000372-T01-IM3 1 0 0 #> P-0000407-T01-IM3 0 0 1 #> P-0000426-T01-IM3 0 0 0 #> P-0000427-T01-IM3 0 0 0 #> P-0000447-T01-IM3 0 0 1 #> P-0000497-T01-IM3 0 0 0 #> P-0000510-T01-IM3 0 0 0 #> P-0000530-T01-IM3 1 0 0 #> P-0000538-T01-IM3 0 0 1 #> P-0000546-T01-IM3 0 0 0 #> P-0000569-T01-IM3 0 0 0 #> P-0000573-T01-IM3 0 0 1 #> P-0000625-T01-IM3 0 0 1 #> P-0000678-T01-IM3 1 0 1 #> P-0000684-T01-IM3 0 0 1 #> P-0000708-T01-IM3 0 0 0 #> P-0000726-T01-IM3 0 0 1 #> P-0000745-T01-IM3 0 0 1 #> P-0000761-T01-IM3 0 0 1 #> P-0000770-T01-IM3 0 0 1 #> P-0000777-T01-IM3 0 0 1 #> P-0000789-T01-IM3 0 1 1 #> P-0000791-T01-IM3 0 0 0 #> P-0000788-T01-IM3 1 0 0 #> P-0000795-T01-IM3 0 0 0 #> P-0000805-T01-IM3 0 0 0 #> P-0000809-T01-IM3 0 0 0 #> P-0000838-T01-IM3 0 0 0 #> P-0000842-T01-IM3 0 0 0 #> P-0000847-T01-IM3 0 0 0 #> P-0000855-T01-IM3 0 0 1 #> P-0000861-T01-IM3 0 0 0 #> P-0000820-T02-IM3 0 0 0 #> P-0000878-T01-IM3 0 0 1 #> P-0000879-T01-IM3 0 1 0 #> P-0000904-T01-IM3 0 1 0 #> P-0000912-T01-IM3 0 0 0 #> P-0000914-T01-IM3 0 0 0 #> P-0000929-T01-IM3 0 0 1 #> P-0000954-T01-IM3 0 1 1 #> P-0001001-T01-IM3 0 0 0 #> P-0001004-T01-IM3 0 0 0 #> P-0001027-T01-IM3 0 0 0 #> P-0001046-T01-IM3 0 0 1 #> P-0001038-T01-IM3 0 0 1 #> P-0000955-T01-IM3 0 0 0 #> P-0001096-T01-IM3 0 0 0 #> P-0001103-T01-IM3 0 0 0 #> P-0000963-T01-IM3 0 0 1 #> P-0001107-T01-IM3 0 0 1 #> P-0001158-T01-IM3 0 0 1 #> P-0001177-T01-IM3 0 0 0 #> P-0001181-T01-IM3 0 0 0 #> P-0001197-T01-IM3 0 0 1 #> P-0001208-T01-IM3 1 0 0 #> P-0001218-T01-IM3 1 0 0 #> P-0001239-T01-IM3 0 1 0 #> P-0001255-T01-IM3 0 0 1 #> P-0001286-T01-IM3 0 0 0 #> P-0001296-T01-IM3 0 0 1 #> P-0001303-T01-IM3 0 0 1 #> P-0001293-T01-IM3 0 0 1 #> P-0001320-T01-IM3 0 0 1 #> P-0001337-T01-IM3 0 0 0 #> P-0001350-T01-IM3 1 0 0 #> P-0001345-T01-IM3 0 0 0 #> P-0000964-T02-IM3 0 0 0 #> P-0001385-T01-IM3 0 0 1 #> P-0001397-T01-IM3 0 0 0 #> P-0001388-T01-IM3 0 1 0 #> P-0001427-T01-IM3 0 0 1 #> P-0001460-T01-IM3 0 0 1 #> P-0001485-T01-IM3 0 1 0 #> P-0000216-T02-IM3 1 0 0 #> P-0001493-T01-IM3 0 0 0 #> P-0001507-T01-IM3 0 0 0 #> P-0001512-T01-IM3 0 0 0 #> P-0001538-T01-IM3 0 1 0 #> P-0001540-T01-IM3 0 0 0 #> P-0001555-T01-IM3 0 0 1 #> P-0001551-T01-IM3 0 0 1 #> P-0001564-T01-IM3 0 0 1 #> P-0001583-T01-IM3 1 0 1 #> P-0001596-T01-IM3 0 0 0 #> P-0001585-T01-IM3 0 0 0 #> P-0001603-T01-IM3 0 1 1 #> P-0001611-T01-IM3 0 0 1 #> P-0001616-T01-IM3 0 0 1 #> P-0001358-T02-IM3 1 1 0 #> P-0001669-T01-IM3 0 0 0 #> P-0001687-T01-IM3 0 0 0 #> P-0001680-T02-IM3 0 1 0 #> P-0001701-T01-IM3 0 0 1 #> P-0001711-T01-IM3 0 0 0 #> P-0001724-T01-IM3 0 0 0 #> P-0001730-T01-IM3 0 0 0 #> P-0001741-T01-IM3 0 0 1 #> P-0001752-T01-IM3 0 0 1 #> P-0001781-T01-IM3 0 0 0 #> P-0001787-T01-IM3 0 0 1 #> P-0001822-T01-IM3 0 0 0 #> P-0001823-T01-IM3 0 0 1 #> P-0001830-T01-IM3 1 0 1 #> P-0001861-T01-IM3 0 0 1 #> P-0001884-T01-IM3 0 0 0 #> P-0001919-T01-IM3 0 0 0 #> P-0001930-T01-IM3 0 0 0 #> P-0001991-T01-IM3 0 1 0 #> P-0002021-T01-IM3 0 0 1 #> P-0001684-T02-IM3 0 0 0 #> P-0002060-T01-IM3 0 0 1 #> P-0002063-T01-IM3 0 1 0 #> P-0002069-T01-IM3 0 0 0 #> P-0000715-T03-IM3 0 1 0 #> P-0002091-T01-IM3 0 0 1 #> P-0002096-T01-IM3 0 0 0 #> P-0001135-T02-IM3 0 1 1 #> P-0002127-T01-IM3 0 0 0 #> P-0002135-T01-IM3 0 0 0 #> P-0002144-T01-IM3 0 0 0 #> P-0002141-T01-IM3 0 1 0 #> P-0002160-T01-IM3 0 0 1 #> P-0002164-T01-IM3 0 0 1 #> P-0002207-T01-IM3 0 0 1 #> P-0000377-T03-IM3 0 0 1 #> P-0002240-T01-IM3 0 0 1 #> P-0002257-T01-IM3 0 0 1 #> P-0002291-T01-IM3 1 0 1 #> P-0002292-T01-IM3 0 1 1 #> P-0002296-T01-IM3 0 0 0 #> P-0002313-T01-IM3 0 0 1 #> P-0002327-T01-IM3 1 0 1 #> P-0002343-T01-IM3 0 0 1 #> P-0002344-T01-IM3 0 1 1 #> P-0002273-T02-IM3 0 0 0 #> P-0002367-T01-IM3 0 1 1 #> P-0002374-T01-IM3 0 0 1 #> P-0002396-T01-IM3 1 1 0 #> P-0002405-T01-IM3 0 1 1 #> P-0002407-T01-IM3 0 0 1 #> P-0002421-T01-IM3 0 0 1 #> P-0002434-T01-IM3 0 0 0 #> P-0002442-T01-IM3 0 0 1 #> P-0002456-T01-IM3 1 0 0 #> P-0002463-T01-IM3 1 0 0 #> P-0002500-T01-IM3 0 0 0 #> P-0002510-T01-IM3 0 1 0 #> P-0002536-T01-IM3 0 0 1 #> P-0002533-T01-IM3 0 0 0 #> P-0002580-T01-IM3 0 0 0 #> P-0002591-T01-IM3 1 0 1 #> P-0002605-T01-IM3 0 0 1 #> P-0002614-T01-IM3 1 0 0 #> P-0002608-T01-IM3 0 0 0 #> P-0002616-T01-IM3 0 0 0 #> P-0002624-T01-IM3 0 0 0 #> P-0002629-T01-IM3 0 0 1 #> P-0002651-T01-IM3 0 0 1 #> P-0002656-T01-IM3 0 0 0 #> P-0002658-T01-IM3 0 0 1 #> P-0002673-T01-IM3 0 0 1 #> P-0001942-T03-IM3 0 0 1 #> P-0002640-T01-IM3 0 0 0 #> P-0002706-T01-IM3 0 1 0 #> P-0002729-T01-IM3 0 0 1 #> P-0002770-T01-IM3 0 0 1 #> P-0002777-T01-IM3 0 1 1 #> P-0002783-T01-IM3 0 0 1 #> P-0002794-T01-IM3 0 0 0 #> P-0002828-T01-IM3 0 0 0 #> P-0002830-T01-IM3 0 0 0 #> P-0002844-T01-IM3 0 0 0 #> P-0002881-T01-IM3 0 0 0 #> P-0002915-T01-IM3 1 0 0 #> P-0002921-T01-IM3 0 0 0 #> P-0002940-T01-IM3 1 0 0 #> P-0002955-T01-IM3 0 0 0 #> P-0002750-T02-IM3 0 0 0 #> P-0002960-T01-IM3 0 0 1
### Considering CNA as well ### bin.mut <- binmat(patients = patients,maf = mut,cna = cna)
#> Warning: MUTATION DATA: To ensure gene with multiple names/aliases are correctly grouped together, the #> following genes in your maf dataframe have been recoded. You can supress this with recode.aliases = FALSE #> #> AMER1 recoded to FAM123B
#> Warning: CNA DATA: To ensure gene with multiple names/aliases are correctly grouped together, the #> following genes in your CNA data have been recoded. You can supress this with recode.aliases = FALSE. #> #> AMER1 recoded to FAM123B
#> Warning: All samples were sequenced on the same platform. #> The specify.plat argument has been overwritten to FALSE.
pathway <- as.data.frame(cbind(c("path1","path1","path2","path3","path4"),c("PIK3CA","KRAS","TERT","TP53","TP53.Del"))) custom_pathway(mat = bin.mut, pathway = pathway)
#> path1 path2 path3 path4 #> P-0000062-T01-IM3 0 0 1 0 #> P-0000065-T01-IM3 0 1 0 0 #> P-0000113-T01-IM3 0 0 1 0 #> P-0000140-T01-IM3 0 0 0 0 #> P-0000145-T01-IM3 1 0 1 0 #> P-0000157-T01-IM3 1 0 0 0 #> P-0000185-T01-IM3 0 0 1 0 #> P-0000088-T01-IM3 0 1 1 0 #> P-0000193-T01-IM3 0 0 0 0 #> P-0000230-T01-IM3 1 0 1 0 #> P-0000231-T01-IM3 0 0 1 0 #> P-0000242-T01-IM3 0 0 1 0 #> P-0000244-T01-IM3 0 0 1 0 #> P-0000270-T01-IM3 0 0 1 0 #> P-0000281-T01-IM3 0 0 0 0 #> P-0000300-T01-IM3 0 0 0 0 #> P-0000329-T01-IM3 0 0 1 0 #> P-0000336-T01-IM3 0 1 1 0 #> P-0000340-T01-IM3 0 0 0 0 #> P-0000363-T01-IM3 0 0 1 0 #> P-0000370-T01-IM3 0 0 1 0 #> P-0000372-T01-IM3 1 0 0 0 #> P-0000407-T01-IM3 0 0 1 0 #> P-0000426-T01-IM3 0 0 0 0 #> P-0000427-T01-IM3 0 0 0 0 #> P-0000447-T01-IM3 0 0 1 0 #> P-0000497-T01-IM3 0 0 0 0 #> P-0000510-T01-IM3 0 0 0 0 #> P-0000530-T01-IM3 1 0 0 0 #> P-0000538-T01-IM3 0 0 1 0 #> P-0000546-T01-IM3 0 0 0 0 #> P-0000569-T01-IM3 0 0 0 0 #> P-0000573-T01-IM3 0 0 1 0 #> P-0000625-T01-IM3 0 0 1 0 #> P-0000678-T01-IM3 1 0 1 0 #> P-0000684-T01-IM3 0 0 1 0 #> P-0000708-T01-IM3 0 0 0 0 #> P-0000726-T01-IM3 0 0 1 0 #> P-0000745-T01-IM3 0 0 1 0 #> P-0000761-T01-IM3 0 0 1 0 #> P-0000770-T01-IM3 0 0 1 0 #> P-0000777-T01-IM3 0 0 1 0 #> P-0000789-T01-IM3 0 1 1 0 #> P-0000791-T01-IM3 0 0 0 0 #> P-0000788-T01-IM3 1 0 0 0 #> P-0000795-T01-IM3 0 0 0 0 #> P-0000805-T01-IM3 0 0 0 0 #> P-0000809-T01-IM3 0 0 0 0 #> P-0000838-T01-IM3 0 0 0 0 #> P-0000842-T01-IM3 0 0 0 0 #> P-0000847-T01-IM3 0 0 0 0 #> P-0000855-T01-IM3 0 0 1 0 #> P-0000861-T01-IM3 0 0 0 0 #> P-0000820-T02-IM3 0 0 0 0 #> P-0000878-T01-IM3 0 0 1 0 #> P-0000879-T01-IM3 0 1 0 0 #> P-0000904-T01-IM3 0 1 0 0 #> P-0000912-T01-IM3 0 0 0 0 #> P-0000914-T01-IM3 0 0 0 0 #> P-0000929-T01-IM3 0 0 1 0 #> P-0000954-T01-IM3 0 1 1 0 #> P-0001001-T01-IM3 0 0 0 0 #> P-0001004-T01-IM3 0 0 0 0 #> P-0001027-T01-IM3 0 0 0 0 #> P-0001046-T01-IM3 0 0 1 0 #> P-0001038-T01-IM3 0 0 1 0 #> P-0000955-T01-IM3 0 0 0 0 #> P-0001096-T01-IM3 0 0 0 0 #> P-0001103-T01-IM3 0 0 0 0 #> P-0000963-T01-IM3 0 0 1 0 #> P-0001107-T01-IM3 0 0 1 0 #> P-0001158-T01-IM3 0 0 1 0 #> P-0001177-T01-IM3 0 0 0 0 #> P-0001181-T01-IM3 0 0 0 0 #> P-0001197-T01-IM3 0 0 1 0 #> P-0001208-T01-IM3 1 0 0 0 #> P-0001218-T01-IM3 1 0 0 0 #> P-0001239-T01-IM3 0 1 0 0 #> P-0001255-T01-IM3 0 0 1 0 #> P-0001286-T01-IM3 0 0 0 0 #> P-0001296-T01-IM3 0 0 1 0 #> P-0001303-T01-IM3 0 0 1 0 #> P-0001293-T01-IM3 0 0 1 0 #> P-0001320-T01-IM3 0 0 1 0 #> P-0001337-T01-IM3 0 0 0 0 #> P-0001350-T01-IM3 1 0 0 0 #> P-0001345-T01-IM3 0 0 0 0 #> P-0000964-T02-IM3 0 0 0 0 #> P-0001385-T01-IM3 0 0 1 0 #> P-0001397-T01-IM3 0 0 0 0 #> P-0001388-T01-IM3 0 1 0 0 #> P-0001427-T01-IM3 0 0 1 0 #> P-0001460-T01-IM3 0 0 1 0 #> P-0001485-T01-IM3 0 1 0 0 #> P-0000216-T02-IM3 1 0 0 0 #> P-0001493-T01-IM3 0 0 0 0 #> P-0001507-T01-IM3 0 0 0 0 #> P-0001512-T01-IM3 0 0 0 0 #> P-0001538-T01-IM3 0 1 0 0 #> P-0001540-T01-IM3 0 0 0 0 #> P-0001555-T01-IM3 0 0 1 0 #> P-0001551-T01-IM3 0 0 1 0 #> P-0001564-T01-IM3 0 0 1 0 #> P-0001583-T01-IM3 1 0 1 0 #> P-0001596-T01-IM3 0 0 0 0 #> P-0001585-T01-IM3 0 0 0 0 #> P-0001603-T01-IM3 0 1 1 0 #> P-0001611-T01-IM3 0 0 1 0 #> P-0001616-T01-IM3 0 0 1 0 #> P-0001358-T02-IM3 1 1 0 0 #> P-0001669-T01-IM3 0 0 0 0 #> P-0001687-T01-IM3 0 0 0 0 #> P-0001680-T02-IM3 0 1 0 0 #> P-0001701-T01-IM3 0 0 1 0 #> P-0001711-T01-IM3 0 0 0 0 #> P-0001724-T01-IM3 0 0 0 0 #> P-0001730-T01-IM3 0 0 0 0 #> P-0001741-T01-IM3 0 0 1 0 #> P-0001752-T01-IM3 0 0 1 0 #> P-0001781-T01-IM3 0 0 0 0 #> P-0001787-T01-IM3 0 0 1 0 #> P-0001822-T01-IM3 0 0 0 0 #> P-0001823-T01-IM3 0 0 1 0 #> P-0001830-T01-IM3 1 0 1 0 #> P-0001861-T01-IM3 0 0 1 0 #> P-0001884-T01-IM3 0 0 0 0 #> P-0001919-T01-IM3 0 0 0 0 #> P-0001930-T01-IM3 0 0 0 0 #> P-0001991-T01-IM3 0 1 0 0 #> P-0002021-T01-IM3 0 0 1 0 #> P-0001684-T02-IM3 0 0 0 0 #> P-0002060-T01-IM3 0 0 1 0 #> P-0002063-T01-IM3 0 1 0 0 #> P-0002069-T01-IM3 0 0 0 0 #> P-0000715-T03-IM3 0 1 0 0 #> P-0002091-T01-IM3 0 0 1 0 #> P-0002096-T01-IM3 0 0 0 0 #> P-0001135-T02-IM3 0 1 1 0 #> P-0002127-T01-IM3 0 0 0 0 #> P-0002135-T01-IM3 0 0 0 0 #> P-0002144-T01-IM3 0 0 0 0 #> P-0002141-T01-IM3 0 1 0 0 #> P-0002160-T01-IM3 0 0 1 0 #> P-0002164-T01-IM3 0 0 1 0 #> P-0002207-T01-IM3 0 0 1 0 #> P-0000377-T03-IM3 0 0 1 0 #> P-0002240-T01-IM3 0 0 1 0 #> P-0002257-T01-IM3 0 0 1 0 #> P-0002291-T01-IM3 1 0 1 0 #> P-0002292-T01-IM3 0 1 1 0 #> P-0002296-T01-IM3 0 0 0 0 #> P-0002313-T01-IM3 0 0 1 0 #> P-0002327-T01-IM3 1 0 1 0 #> P-0002343-T01-IM3 0 0 1 0 #> P-0002344-T01-IM3 0 1 1 0 #> P-0002273-T02-IM3 0 0 0 0 #> P-0002367-T01-IM3 0 1 1 0 #> P-0002374-T01-IM3 0 0 1 0 #> P-0002396-T01-IM3 1 1 0 0 #> P-0002405-T01-IM3 0 1 1 0 #> P-0002407-T01-IM3 0 0 1 0 #> P-0002421-T01-IM3 0 0 1 0 #> P-0002434-T01-IM3 0 0 0 0 #> P-0002442-T01-IM3 0 0 1 0 #> P-0002456-T01-IM3 1 0 0 0 #> P-0002463-T01-IM3 1 0 0 0 #> P-0002500-T01-IM3 0 0 0 0 #> P-0002510-T01-IM3 0 1 0 0 #> P-0002536-T01-IM3 0 0 1 0 #> P-0002533-T01-IM3 0 0 0 0 #> P-0002580-T01-IM3 0 0 0 0 #> P-0002591-T01-IM3 1 0 1 1 #> P-0002605-T01-IM3 0 0 1 0 #> P-0002614-T01-IM3 1 0 0 0 #> P-0002608-T01-IM3 0 0 0 0 #> P-0002616-T01-IM3 0 0 0 0 #> P-0002624-T01-IM3 0 0 0 0 #> P-0002629-T01-IM3 0 0 1 0 #> P-0002651-T01-IM3 0 1 1 0 #> P-0002656-T01-IM3 0 0 0 0 #> P-0002658-T01-IM3 0 0 1 0 #> P-0002673-T01-IM3 0 0 1 0 #> P-0001942-T03-IM3 0 0 1 0 #> P-0002640-T01-IM3 0 0 0 0 #> P-0002706-T01-IM3 0 1 0 0 #> P-0002729-T01-IM3 0 0 1 0 #> P-0002770-T01-IM3 0 0 1 0 #> P-0002777-T01-IM3 0 1 1 0 #> P-0002783-T01-IM3 0 0 1 0 #> P-0002794-T01-IM3 0 0 0 0 #> P-0002828-T01-IM3 0 0 0 0 #> P-0002830-T01-IM3 0 0 0 0 #> P-0002844-T01-IM3 0 0 0 0 #> P-0002881-T01-IM3 0 0 0 0 #> P-0002915-T01-IM3 1 0 0 0 #> P-0002921-T01-IM3 0 0 0 0 #> P-0002940-T01-IM3 1 0 0 0 #> P-0002955-T01-IM3 0 0 0 0 #> P-0002750-T02-IM3 0 1 0 0 #> P-0002960-T01-IM3 0 0 1 0