readXVcf: Read a vcf file to extract information relevant to XCI
In SRenan/XCIR: XCI-inference

Description Usage Arguments Value References Examples

Read a given vcf file and extract minimum information required for the estimation of the expression of inactivated X chromosome.

1	readXVcf(vcf_file, haps_file = NULL, rm_homo = TRUE)

`vcf_file`	A `character`. The path to a vcf file.
`haps_file`	A `character`. The path to a .haps file, the output of the shapeit software.
`rm_homo`	A `logical`. If set to TRUE, homozygous sites will be removed from the output. Otherwise, they will be set to NA.

A data.table object in long format of length sample*site.

O. Delaneau, B. Howie, A. Cox, J-F. Zagury, J. Marchini (2013) Haplotype estimation using sequence reads. American Journal of Human Genetics 93 (4) 787-696.

# 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)