readRNASNPs {XCIR} | R Documentation |
Read SNPs from RNA-Seq that have not been phased.
readRNASNPs(vcf_file)
vcf_file |
A |
For phased samples, use readXVcf
.
A data.table
of allele specific read counts.
# Example workflow for documentation vcff <- system.file("extdata/AD_example.vcf", package = "XCIR") # Reading functions vcf <- readRNASNPs(vcff) vcf <- readVCF4(vcff) # Annotation functions # Using seqminer (requires additional annotation files) anno <- addAnno(vcf) # Using biomaRt anno <- annotateX(vcf) # Do not remove SNPs with 0 count on minor allele anno0 <- annotateX(vcf, het_cutoff = 0) # Summarise read counts per gene # Assuming data is phased, reads can be summed across genes. genic <- getGenicDP(anno, highest_expr = FALSE) # Unphased data, select SNP with highest overall expression. genic <- getGenicDP(anno, highest_expr = TRUE)