clafProfile: Composite Minor Allele Frequency (CLAF) Profile plot

In JEFworks/badger: Bayesian approach for detecting copy number alterations from single cell RNA-seq data

Description

Composite Minor Allele Frequency (CLAF) Profile plot

Usage

clafProfile(r, n.sc, l, n.bulk, region = NULL, filter = TRUE, delim = ":",
  gtf = NULL, plotGene = FALSE)

Arguments

r	Alt allele count in single cells
n.sc	Coverage in single cells
l	Alt allele count in bulk
n.bulk	Coverage in bulk
region	Restrict plotting to select region. Optional. Default: NULL
filter	Boolean of whether to filter for SNPs with coverage. Default: TRUE
delim	Delimiter for names of SNPs as Chromosome[delim]Position. Default: ":" ex. chr1:283838897
gtf	GTF file contents for mapping SNPs to genes. Required if plotGene = TRUE
plotGene	Boolean of whether to plot gene track. Default: FALSE

Examples

## Single cell data
data(snpsHet_MM16ScSample)
## Bulk exome
data(snpsHet_MM16BulkSample)
# intersect
region <- data.frame('chr'=2, start=0, end=1e9) # deletion region
clafProfile(r, cov.sc, l, cov.bulk, region)
region <- data.frame('chr'=3, start=0, end=1e9) # neutral region
clafProfile(r, cov.sc, l, cov.bulk, region)

JEFworks/badger documentation built on May 7, 2019, 7:40 a.m.