load.exp.RNASeq.demoSalmon: Load Gene Expression Set from Salmon Output (demo version)

In jyyulab/NetBID: Network-based Bayesian Inference of Drivers, version 2

Load Gene Expression Set from Salmon Output (demo version)

Description

load.exp.RNASeq.demoSalmon is a function to read in Salmon results and convert it to eSet/DESeqDataSet class object.

Usage

load.exp.RNASeq.demoSalmon(
  salmon_dir = NULL,
  tx2gene = NULL,
  use_phenotype_info = NULL,
  use_sample_col = NULL,
  use_design_col = NULL,
  return_type = "tpm",
  merge_level = "gene"
)

Arguments

salmon_dir	character, the directory to save the results created by Salmon.
tx2gene	data.frame or NULL, this parameter will be passed to tximport. For details, please check tximport. If NULL, will read in one of the transcript names from Salmon's results. Note, it works when using e.g. "gencode.v29.transcripts.fa" from GENCODE as reference.
use_phenotype_info	data.frame, the data frame contains phenotype information. It must have the columns use_sample_col and use_design_col.
use_sample_col	character, the column name, indicating which column in use_phenotype_info should be used as the sample name.
use_design_col	character, the column name, indicating which column in use_phenotype_info should be used as the design feature for samples.
return_type	character, the class of the return object. "txi" is the output of tximport. It is a list containing three matrices, abundance, counts and length. "counts" is the matrix of raw count. "tpm" is the raw tpm. "fpm", "cpm" is the fragments/counts per million mapped fragments (fpm/cpm). "raw-dds" is the DESeqDataSet class object, which is the original one without processing. "dds" is the DESeqDataSet class object, which is processed by DESeq. "eset" is the ExpressionSet class object, which is processed by DESeq and vst. Default is "tpm".
merge_level	character, users can choose between "gene" and "transcript". "gene", the original salmon results will be mapped to the transcriptome and the expression matrix will be merged to the gene level. This only works when using e.g. "gencode.vXX.transcripts.fa" from GENCODE as the reference.

Details

This function helps users to read in results created by Salmon. Due to the complicated manipulations (e.g. reference sequence) in processing Salmon, this demo function may not be suitable for all scenarios.

jyyulab/NetBID documentation built on Dec. 23, 2024, 6:34 a.m.