snpeff_to_long: snpEff Summary to Long

In BrentLab/brentlabRnaSeqTools: Management/QC for brentlab RNAseq data

snpEff Summary to Long

Description

Transform a snpEff tsv summary frame to long format

Usage

snpeff_summary_to_long(
  snpeff_summary_path,
  sample_id,
  variant_caller,
  effect_threshold = 0,
  impact_threshold = 0
)

Arguments

snpeff_summary_path	path to the .txt summary output of snpEff
sample_id	unique identifier of this sample – sample_id becomes a column
variant_caller	the variant caller used to create the vcf
effect_threshold	minimum count in a variant_effect factor level (see the seealso link below for the snpEff docs if variant_effect factor doesn't ring a bell)
impact_threshold	minimum count in a variant_impact factor level (see the command in effect_threshold)

Value

a tibble with the fields GeneId, TranscriptId, Biotype, effect, effect_score, impact_score, impact, sample_id, variant_caller

See Also

https://pcingola.github.io/SnpEff/se_outputsummary/

Examples

## Not run: 
if(interactive()){
 #EXAMPLE1
 }

## End(Not run)

BrentLab/brentlabRnaSeqTools documentation built on Aug. 20, 2023, 9:22 a.m.