trapdiff: Run trapdiff and save report file

In paulklemm/trapdiff: Differential Gene Expression for bacTRAP/riboTRAP data based on DESeq2

Run trapdiff and save report file

Description

Run trapdiff and save report file

Usage

trapdiff(
  counts,
  path_config_json,
  out_path,
  ensembl_version = 102,
  biotypes_filter = "",
  tpms_min = 0,
  padj_cutoff = 0.05,
  save_rds = TRUE,
  save_excel = TRUE,
  save_figures = TRUE,
  deseq_split_size_factors = FALSE,
  splits = "treatment",
  filter_regex = "^mt-"
)

Arguments

counts	Counts per sample as dataframe
path_config_json	Configuration file telling trapdiff group associations
out_path	Output folder for report and intermediate files
ensembl_version	Ensembl version used for attaching biomart variables
biotypes_filter	Filter genes for these biotypes. Put empty string for no filtering.
tpms_min	A gene is included when at least one sample contains tpms_min reads
padj_cutoff	Minimum padj value for a significantly differentially expressed gene
save_rds	Save rds file of results
save_excel	Save Excel sheets of results
save_figures	Save output figures as png and pdf in out_path/figures
deseq_split_size_factors	Create sizeFactor estimates separately for each split condition
splits	If deseq_split_size_factors is set to true, sizeFactors are calculated for these groups separately
filter_regex	Manually regex out genes. Defaults to all mitochondrial genes starting with "mt-"

paulklemm/trapdiff documentation built on Nov. 12, 2022, 12:12 a.m.