filter_junc: Filter junctions using count and acceptor/donor annotation

In dzhang32/RNAdiagnosR: What the Package Does (One Line, Title Case)

Description

filter_junc takes as input raw and normalised counts, then applies both a count and acceptor/donor filter.

Usage

filter_junc(raw_counts, norm_counts, junc_count_filter, junc_metadata,
  annot_AD_filter = c("none", "ambig"), filter_ambig_gene = T)

Arguments

raw_counts	df. Detailing the raw counts for each junction. Rows as junctions, cols as samples, values as raw counts.
norm_counts	df. Detailing the normalised counts for each junction. Rows as junctions, cols as samples, values as raw counts.
junc_count_filter	lgl vector. Returned from get_junc_count_filter.
junc_metadata	df. Detailing the metadata of the columns, must include "annot_AD" column with whether junc has an acceptor or donor site overlapping a known exon.
annot_AD_filter	int scalar. Which types of annotation to exclude. Default is "none" or "ambig"

Value

list. Raw, normalised counts and metadata data filtered.

dzhang32/RNAdiagnosR documentation built on Dec. 5, 2019, 2 a.m.