# M1-get_assnp_local
## ==================================================================================
## Function: get_assnp_local
### Aim: To get allele-specific SNP using local file
### INPUT 1: index SNP list (a .csv file), with the 1st col the rsID and the 2nd col Population
### INPUT 2: snp information table (a .csv file), contains column names with rsID and population
### OUTPUT: potential allele-specific effect (ase) snps
## ==================================================================================
# source function
# source("./src/scripts/M1-get_assnp.R")
# wrapper function: get_assnp_byBam ---------------------------------------------------------------------------
# get ase snp just by .bam files, not using .vcf files; no information of peak, and cnv added
get_assnp_byBam = function(index_snp_file,
snp_info_file = NA,
sample_name = "",
bam_dir,
merge_replicates = F) {
get_assnp(index_snp_file = index_snp_file,
snp_info_file = snp_info_file,
sample_name = sample_name,
bam_dir = bam_dir,
genotype_by_sample = F,
merge_replicates = merge_replicates)
}
# Test #
# get_assnp_singleBam(index_snp_file = "./data/input_snps/LUC_Index_SNPs_20160607_short.csv",
# bam_dir = "./data/samples/DDBJ_A549/bam_files/", sample_name = "A549_singleBam")
# wrapper function: get_assnp_sample ------------------------------------------------------------------------------
# get ase snp just by .bam files and .vcf files; with information of peak, and cnv added; ase are corrected by cnv
get_assnp_bySample = function(index_snp_file,
snp_info_file = NA,
sample_name = "",
sample_dir = "./data/samples/DDBJ_A549/",
merge_replicates = F) {
bam_dir = paste0(sample_dir, "/bam_files/")
peak_dir = paste0(sample_dir, "/peak_files/")
vcf_dir = paste0(sample_dir, "/vcf_files/")
vcf_file_for_cnv = list.files(vcf_dir, "[Ww][Gg][Ss].*vcf$", full.names = T)
get_assnp(index_snp_file = index_snp_file,
snp_info_file = snp_info_file,
sample_name = sample_name,
bam_dir = bam_dir,
peak_dir = peak_dir,
vcf_dir = vcf_dir,
vcf_file_for_cnv = vcf_file_for_cnv,
genotype_by_sample = T,
merge_replicates = merge_replicates)
}
# get_assnp_sample(index_snp_file = "./data/input_snps/LUC_Index_SNPs_20160607.csv",
# sample_name = "A549_bySample", sample_dir = "./data/samples/DDBJ_A549/")
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