post_process_salmon: post_process_salmon

In Benjamin-Vincent-Lab/StarSalmon: Functions for writing commands and post processing the Star Salmon pipeline.

post_process_salmon

Description

Joins individual sample files into one tsv file. Also converts ucsc names to hgnc_symbol|entrez_ids and outputs the gene level counts.

Usage

post_process_salmon(this_script_path = "", input_file_paths, output_dir,
  ref = "grch38", gene_biotypes = c("protein_coding",
  "from AnnotationDbi", "IG_C_gene", "IG_D_gene", "IG_J_gene", "IG_V_gene",
  "TR_C_gene", "TR_D_gene", "TR_J_gene", "TR_V_gene"),
  output_transcript_matrix = TRUE, output_hgnc_matrix = TRUE,
  output_entrez_id_matrix = FALSE,
  output_piped_hugo_entrez_id_matrix = FALSE,
  output_upper_quartile_norm = TRUE,
  output_log2_upper_quartile_norm = TRUE, counts_or_tpm = "counts")

Arguments

this_script_path	Path to script that runs this function for documentation urposes
input_file_paths	Named character vector of paths to the pipeline output data. Samples will be named by the names of the vector. If not named thye will be named after the quant file.
output_dir	Path to the output folder.
ref	options 'grch38' with ensemble output or 'hg38' with ucsc output
gene_biotypes	The type of biomaRt gene_biotypes that should be output to the gene level output.
output_transcript_matrix	T/F
output_hgnc_matrix	T/F
output_entrez_id_matrix	T/F
output_piped_hugo_entrez_id_matrix	T/F
output_upper_quartile_norm	T/F
output_log2_upper_quartile_norm	T/F
counts_or_tpm	'counts' or 'tpm'

Details

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ post_process_salmon ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Value

A vector of paths to the files.

See Also

Other mart: get_biomart_grch38_path, get_biomart_hg38_path

Benjamin-Vincent-Lab/StarSalmon documentation built on Feb. 15, 2024, 11:34 p.m.