annotateX: Annotate
In SRenan/XCIR: XCI-inference

Description Usage Arguments Value Examples

Map positions of SNPs to genes extracted from biomaRt

annotateX(
  xciObj,
  read_count_cutoff = 20,
  het_cutoff = 3,
  release = "hg38",
  mirror = NULL,
  verbose = FALSE
)

`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.

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