annotateX: Annotate

Description Usage Arguments Value Examples

View source: R/annotate.R

Description

Map positions of SNPs to genes extracted from biomaRt

Usage

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annotateX(xciObj, read_count_cutoff = 20, het_cutoff = 3,
  release = "hg19", verbose = FALSE)

Arguments

xciObj

A data.table. The data to be annotated must contain at least the 4 columns 'GENE', 'POS', 'AD_hap1', 'AD_hap2'. Additional columns will be preserved.

read_count_cutoff

A numeric. Keep only SNPs that have at least that many reads.

het_cutoff

A numeric. Keep only SNPs that have at least that many reads on each allele.

release

A character. Genome release name. Valid releases are "hg19", "hg38".

verbose

A logical. If set to TRUE, print additional information.

Value

A data.table. The input table annotated with gene symbols and filtered for read counts.

Examples

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# 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)

XCIR documentation built on Nov. 8, 2020, 7:41 p.m.