cannot change ref_genome in sig_tally

[JanSliacky]

Hi, I am trying to change ref_genome attribute to BSgenome.Hsapiens.UCSC.hg38. I install the ref_genome using BiocManager::install("BSgenome.Hsapiens.UCSC.hg38")

I downloaded the human_hg38_gene_info.rds file and put it into proper directory

However, when running the sig_tally(), it still uses the hg19 - see here:
Annotating mutations to first matched gene based on database /home/pc1/R/x86_64-pc-linux-gnu-library/4.3/sigminer/extdata/human_hg19_gene_info.rds...

Can you help me and tell me what is the problem?

[ShixiangWang]

Hi, have you set ref_genome = "BSgenome.Hsapiens.UCSC.hg38"？ Could you show more of your commands?

[JanSliacky]

This is the code:

# libraries
library(BSgenome.Hsapiens.UCSC.hg38)
library(sigminer)
library(tidyverse)
library(magrittr)
library(pheatmap)
library(kableExtra)

# setting the working directories
setwd("~/signatury/EGA/subory/unzip/selected/vcfs/")
vcfs <- list.files(".", "*.vcf", full.names = FALSE)

# loop to get maf file
mtf <- data.frame()
for (i in 1:length(vcfs)) {
  m <- read_vcf(vcfs[i], keep_only_pass = FALSE) 
  mt_tally <- sig_tally(
    m,
    ref_genome = "BSgenome.Hsapiens.UCSC.hg38",
    use_syn = TRUE,
    cores = 16
  )
  mtf <- rbind(mtf, mt_tally$nmf_matrix)
}

This is the log:

> for (i in 1:length(vcfs)) {
+   m <- read_vcf(vcfs[i], keep_only_pass = FALSE) 
+   mt_tally <- sig_tally(
+     m,
+     ref_genome = "BSgenome.Hsapiens.UCSC.hg38",
+     use_syn = TRUE,
+     cores = 16
+   )
+   mtf <- rbind(mtf, mt_tally$nmf_matrix)
+ }
Reading file(s): CRUK0037_BS_GL_selected.vcf
Annotating Variant Type...
Annotating mutations to first matched gene based on database /home/pc1/R/x86_64-pc-linux-gnu-library/4.3/sigminer/extdata/human_hg19_gene_info.rds...
Transforming into a MAF object...
-Validating
--Non MAF specific values in Variant_Classification column:
  Unknown
-Summarizing
-Processing clinical data
--Missing clinical data
-Finished in 6.452s elapsed (8.630s cpu) 

[JanSliacky]

sig_tally.MAF <- function(object, mode = c("SBS", "DBS", "ID", "ALL"), ref_genome = "BSgenome.Hsapiens.UCSC.hg19", genome_build = NULL, add_trans_bias = FALSE, ignore_chrs = NULL, use_syn = TRUE, keep_only_matrix = FALSE, ...) {

It looks like it is hardcoded in the function. See: https://github.com/ShixiangWang/sigminer/blob/master/R/sig_tally.R

[ShixiangWang]

Hi, you used the read_vcf, please set the option to "hg38" in this function. You set the sig_tally() correctly. :)

sigminer/R/read_vcf.R

Line 24 in d802c14

genome_build = c("hg19", "hg38", "mm10", "mm9", "ce11"),

[JanSliacky]

many thanks for your help. It works now perfectly.