rnahapsNearGene: produce a GRanges with RNA haplotypes near a specific gene

In vjcitn/BiocRnaHap: explore RNA-seq based haplotyping using Phaser

Description

produce a GRanges with RNA haplotypes near a specific gene

Usage

rnahapsNearGene(sym, haptab = NA06986_rnahaps,
  genes = ensembldb::genes(EnsDb.Hsapiens.v75::EnsDb.Hsapiens.v75),
  radius = 10000, min_total_reads = 15, min_variants = 2,
  varnum_to_use = 2:6)

Arguments

sym	character(1) gene symbol
haptab	data.frame corresponding to phaser haplotypes.txt table
genes	a GRanges as produced by ensembldb::genes
radius	numeric(1) interval upstream and downstream to be included with gene region for selection of RNA haplotypes
min_total_reads	numeric(1) lower bound on number of reads needed to retain a haplotype
min_variants	lower bound on number of variants in the haplotype to warrant retention
varnum_to_use	the values of the 'variants' field for which records are retained

Note

grep() is used with fixed=TRUE to find sym in genes()$gene_name

Examples

rnahapsNearGene("GSDMB")

vjcitn/BiocRnaHap documentation built on June 17, 2019, 9:31 p.m.