When I executed the "batchCallGeno" function as flow, an error occurred: operator is invalid for atomic vectors.

geno_out <- batchCallGeno(GT_flt, CHROM = CHROM, 
                     pos.start = 7, fix.size = 10)

This error Can't be solved by translating GT_flt(matrix) to dafa.frame.
The problem is created by the "batchCallGeno" function,

Call Geno by window

  geno <- callWindowGeno(x, window.size = window.size,
                         low = low.count, high = high.count)

  ## Fix the potential error
  geno_fix <- fixGenoError(geno, fix.size = fix.size)

The Key

After "callWindowGeno", the geno is a list. But the "fixGenoError" function tries to quote the colnames (geno, CHROM and ind.name) that don't exist in geno. And the "callWindowGeno" function doesn't generate these colnames.

fixGenoError function

 fixGenoError <- function(x, fix.size = 10 ){
 
   geno <- x$geno
   chroms <- x$CHROM
   samples <- x$ind.name

callWindowGeno

callWindowGeno <- function(x, window.size = 15,
                           low = 6, high = 24){

  splitSNP <- split(x, ceiling(seq_along(x)/window.size))

  batchSNP <- sapply(seq_along(splitSNP), function(x){

    snp_num <- length(splitSNP[[x]])
    start_name <- names(splitSNP[[x]][1])
    end_name <- names(splitSNP[[x]][snp_num])

    chr_name <- strsplit(start_name,"_",fixed = TRUE)[[1]][1]
    start_pos <- as.numeric(strsplit(start_name,"_",fixed = TRUE)[[1]][2])
    end_pos <- as.numeric(strsplit(end_name,"_",fixed = TRUE)[[1]][2])

    total <- sum(splitSNP[[x]], na.rm = TRUE)
    names(total) <- paste(chr_name, floor((start_pos + end_pos) / 2) , sep = "_")
    return(total)
  })

  geno <- ifelse(batchSNP < low, 0, ifelse(batchSNP > high ,2 , 1))

  return(geno)
}

install.packages("binmapr")
Installing package into ‘/home/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
Warning in install.packages :
package ‘binmapr’ is not available for this version of R
Thanks

When I run the example you provide, it occurred an error?

The operation process is as follows:

AD <- matrix(data = c("30,1","1,30","0,0","15,15"), nrow = 2)
row.names(AD) <- c("chr1_1","chr1_100")
colnames(AD) <- c("A","B")
freq <- calcFreqFromAd(AD)
Error: $ operator is invalid for atomic vectors

I have tried trun the matrix to data.frame, but it doesn't work. I wish if you can help me to solve this problem.

Dear Gengxin Xu，

I am using the relevant code of Baidu Netdisk, which can successfully run the sample data, but the following error always appears in my data set. Can you please help me solve it?

Yours sincerely

Yan Qiu

freq <- calcFreqFromAd(ad_flt, min.depth = 10, max.depth = 100)
错误: $ operator is invalid for atomic vectors