get_case_mean_coverage: Compute the mean coverage of a CASE sample

In cibiobcg/abemus: Adaptive Base Error Model in Ultra-Deep Sequencing Data

Compute the mean coverage of a CASE sample

Description

Compute the mean coverage of a CASE sample

Usage

get_case_mean_coverage(tabindex, pacbamfolder_bychrom)

Arguments

tabindex	The data.frame output by the callsnvs function.
pacbamfolder_bychrom	The folder popluted by outputs by the split_pacbam_bychrom function.

Value

The sample.info.file with an additional column reporting the mean coverage for each case (only for those with a matched-CONTROL)

Examples

sample.info.file <- system.file("extdata", "test_sif_toy.tsv", package = "abemus")
outdir <- tempdir()
targetbed <- system.file("extdata", "regions_toy.bed", package = "abemus")
pacbamfolder_bychrom <- system.file("extdata", "pacbam_data_bychrom", package = "abemus")
pbem_dir <- system.file("extdata", "BaseErrorModel", package = "abemus")
controls_dir <- system.file("extdata", "Controls", package = "abemus")
m<-callsnvs(sample.info.file,outdir,targetbed,pbem_dir,controls_dir,pacbamfolder_bychrom,replicas=1)
tabindex <- m$tabsnvs_index
tabindex <- get_case_mean_coverage(tabindex = tabindex,pacbamfolder_bychrom = pacbamfolder_bychrom)

cibiobcg/abemus documentation built on Oct. 29, 2022, 9:03 p.m.