import_tx: Import Expression Data

In luciorq/txomics: Functional Analysis and Visualization of Transcriptomic Data

Description

Function used to import transcripts count and abundance data

Usage

import_tx(path, source = "salmon", accession = "vectorbase",
  is_dir = TRUE, names = NULL, gene_table = NULL)

Arguments

path	path to files, or vector of paths, if is_dir is set to FALSE
source	quantification method used. Currently supported: "salmon", "kallisto". If method is unknown use "none".
accession	source of gene names identifier supported formats:"vectorbase", "gene", "custom" If using "gene", the trancript names will be used as genes; If using "custom", a conversion table should be provided in the gene_table parameter; not supported yet: "ensembl", "ncbi", "custom"
is_dir	if path is a directory containing subdirectories with the files, if is_dir is set to FALSE, path should be a vector of paths; default = TRUE
names	.vector of names to be used to each sample; default = NULL
gene_table	a transcript to gene conversion table, where the first column should be transcript name and the second column should be gene name, should only be used with accession = "custom"

Value

A txi object containing

Examples

## Not run: 
# Example with path to folder input
imported_transcripts <- import_tx("data/salmon/quants/")

## End(Not run)

luciorq/txomics documentation built on Sept. 3, 2020, 5:36 a.m.