Build a custom modulelist

Build a custom modulelist

Transform a modulelist to a list

custom_modulelist(pathway2ko, pathway2desc = NULL, verbose = TRUE)

transform_modulelist(mymodulelist, mode = 1)

Arguments

pathway2ko

user input annotation of Pathway to KO mapping, a data.frame of 2 column with pathway and ko.

pathway2desc

user input of Pathway TO Description mapping, a data.frame of 2 column with pathway and description.

verbose

verbose

mymodulelist

mymodulelist

mode

1~2

Value

a custom modulelist

modulelist

See also

Other modulelist: custom_modulelist_from_org(), get_features()

Other modulelist: custom_modulelist_from_org(), get_features()

Examples

mydat <- data.frame(pathway = paste0("PATHWAY", rep(seq_len(2), each = 5)), ko = paste0("K", 1:10))
mymodulelist <- custom_modulelist(mydat)
#> please assgin this custom modulelist to `reporter_score(modulelist=your_modulelist)` to do a custom enrichment.
print(mymodulelist)
#>         id K_num             KOs Description
#> 1 PATHWAY1     5  K1,K2,K3,K4,K5    PATHWAY1
#> 2 PATHWAY2     5 K6,K7,K8,K9,K10    PATHWAY2
transform_modulelist(mymodulelist)
#> $PATHWAY1
#> [1] "K1" "K2" "K3" "K4" "K5"
#> 
#> $PATHWAY2
#> [1] "K6"  "K7"  "K8"  "K9"  "K10"
#>