load.exp.RNASeq.demo: Load Gene Expression Set from RNA-Seq Results (demo version)

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

Load Gene Expression Set from RNA-Seq Results (demo version)

Description

load.exp.RNASeq.demo is a function to read in RNA-Seq results and convert it to eSet/DESeqDataSet class object.

Usage

load.exp.RNASeq.demo(
  files,
  type = "salmon",
  tx2gene = NULL,
  use_phenotype_info = NULL,
  use_sample_col = NULL,
  use_design_col = NULL,
  return_type = "tpm",
  merge_level = "gene"
)

Arguments

files	a vector of characters, the filenames for the transcript-level abundances. It will be passed to tximport. For details, please check tximport.
type	character, the type of software used to generate the abundances. It will be passed to tximport. For details, please check tximport.
tx2gene	data.frame or NULL, this parameter will be passed to tximport. For details, please check tximport.
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. "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 RNA-Seq results from various sources. Due to the complicated manipulations (e.g. reference sequence) in processing RNA-Seq, this demo function may not be suitable for all scenarios.

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