post_process_mixcr: post_process_star_salmon

In DanteBortone/MiXCR: Functions for writing commands and post processing the MiXCR 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_mixcr(input_file_paths, output_dir, sample_data_path,
  my_chains = my_chains, sample_folder_column = "Sample_Folder",
  sample_id_column = "Sample_ID", thread_num = 1)

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
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
gene_biotypes	The type of biomaRt gene_biotypes that should be output to the gene level output.

Details

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

Value

A path to the rds file.

DanteBortone/MiXCR documentation built on Aug. 14, 2022, 2:41 p.m.