post_process_star_salmon: post_process_star_salmon

In DanteBortone/StarSalmon: Functions for writing commands and post processing the Star Salmon pipeline.

post_process_star_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_star_salmon(input_file_paths, output_dir, sample_data_path,
  gene_biotypes = c("IG_C_gene", "IG_D_gene", "IG_J_gene", "IG_V_gene",
  "misc_RNA", "processed_transcript", "protein_coding", "TR_C_gene",
  "TR_D_gene", "TR_J_gene", "TR_V_gene", "lincRNA"),
  sample_folder_column = "Sample_Folder",
  sample_id_column = "Sample_ID", thread_num = 16)

Arguments

input_file_paths	Character vector of paths to the pipeline output data.
output_dir	Path to the output folder.
sample_data_path	Path to the sample data which should contatin the sample_id_column and sample_folder_column
gene_biotypes	The type of biomaRt gene_biotypes that should be output to the gene level output.
sample_folder_column	The name of the column that has sample folder names
sample_id_column	The name of the column that has sample ids
thread_num	Integer number of threads to run mclapply statements

Details

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ post_process_star_salmon ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Value

A path to the rds file.

See Also

Other mart: get_biomart_hsa_ucsc_path

DanteBortone/StarSalmon documentation built on Aug. 16, 2022, 9:33 a.m.