Subscript out of bounds error at momaObj$Rank() step

[heathergeiger]

I am getting the following error at momaObj$Rank() step:

Error in pathway[[as.character(tf)]] : subscript out of bounds Calls: ... pathwayDiggitIntersect -> -> lapply -> FUN

Attached please find my input matrices. Row names are Entrez IDs. Code below.

MOMA_input_cnv.txt MOMA_input_mut.txt MOMA_input_viper.txt

library(MOMA)

viper <- read.csv("Results_for_paper_March_2021/MOMA_input_viper.txt",header=TRUE,row.names=1,check.names=FALSE)
cnv <- read.csv("Results_for_paper_March_2021/MOMA_input_cnv.txt",header=TRUE,row.names=1,check.names=FALSE)
mut <- read.csv("Results_for_paper_March_2021/MOMA_input_mut.txt",header=TRUE,row.names=1,check.names=FALSE)

load("pvals-prad.rda")

momaObj <- MomaConstructor(x=list(viper = as.matrix(viper),cnv = as.matrix(cnv),mut = as.matrix(mut)),pathways=cindy.list)

momaObj$runDIGGIT()
momaObj$makeInteractions()
momaObj$Rank()

[heathergeiger]

Here is the full set of error messages for the above script: Found the following assays:viper, cnv, mut Number of samples in VIPER + Mutation data: 49 Number of samples in VIPER + CNV data: 49 Checking labels on pathway 10001 Found labels for 719 TFs in VIPER matrix Checking labels on pathway 10002 Found labels for 960 TFs in VIPER matrix [... for other TFs] No fCNV supplied, using no CNV filter! Found 974 significant TFs from VIPER scores ... Building background model from 3625 nulls... Performing background correction for Amplifications NES scores... Generating final interactions... Performing background correction for Deletions NES scores... Generating final interactions... Performing background correction for Mutations NES scores... Generating final interactions... Performing background correction for Fusions NES scores... Error in pathway[[as.character(tf)]] : subscript out of bounds Calls: ... pathwayDiggitIntersect -> -> lapply -> FUN Execution halted