readRNASNPs: Read SNPs from RNA-Seq
In SRenan/XCIR: XCI-inference

Description Usage Arguments Details Value Examples

Read SNPs from RNA-Seq that have not been phased.

1	readRNASNPs(vcf_file)

vcf_file

A character. The path to a vcf file.

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, mirror = "useast")
# Do not remove SNPs with 0 count on minor allele
anno0 <- annotateX(vcf, het_cutoff = 0, mirror = "useast")

# 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)