JCNAprepare: JCNAprepare: WGCNA annotation for junction expression-based...

In MauerLab/DJExpress: An integrated application for differential splicing analysis and visualization

Description

Filters samples and junctions in DJEanalyze expression data object for junction co-expression network analysis.

Usage

JCNAprepare(
  input.type = c("DJEanalyze.out", "junction.counts"),
  workDir = NULL,
  data.type = c("sample", "matrix"),
  aligner = c("STAR", "other"),
  analize.out = NULL,
  Group1 = NULL,
  gtf = NULL,
  minMean = 10,
  maxMean = Inf,
  minVar = 0,
  maxVar = Inf,
  calcNormFactors = FALSE,
  calMethod = "none",
  MVtrend.plot = FALSE,
  traitData = NULL,
  TSdendrogram = FALSE,
  nThreads = 2,
  abline.threshold = NULL
)

Arguments

input.type	input object type. Options are DJEanalyze() output object or junction read counts table.
workDir	path to folder where individual junction quantification files (e.g. from STAR alignment) are located. This folder should only contain junction quantification files.
data.type	One of c("sample", "matrix"), indicating whether the input files are matrices per individual samples or joint into a single expression matrix. Only used when input.type = "junction.counts".
aligner	One of c("STAR", "other"), indicating the alignment tool used to produce junction quantification. Only used if data.type = "matrix". #' If "other" is indicated, files in workDir path should contain junction IDs (with the format chr:start:end:strand) in the first column read counts in the second column.
analize.out	output object from DJEanalyze(). Only used if input.type = "DJEanalyze.out".
Group1	vector or factor specifying basic control sample names. Only used if input.type = "DJEanalyze.out".
gtf	Reference transcriptome in genecode gtf file format. Used to define gene ID for junctions if input.type = "junction.counts".
minMean	numeric: minimum of read count mean per junction. Only used if input.type = "junction.counts".
maxMean	numeric: maximum of read count mean per junction. Only used if input.type = "junction.counts".
minVar	numeric: minimum of read count variance per junction. Only used if input.type = "junction.counts".
maxVar	numeric: maximum of read count variance per junction. Only used if input.type = "junction.counts".
calcNormFactors	logical, should edgeR's library Size Normalization be calculated?. Only used if input.type = "junction.counts".
calMethod	Normalization method to be used. Options are: "TMM","RLE","upperquartile" or "none" (default "none"). Only used if input.type = "junction.counts".
MVtrend.plot	logical, should median/variance trend plot be displayed?. Only used if input.type = "junction.counts".
traitData	a numeric vector or a matrix of external sample traits. Samples should be as rows and traits as columns.
TSdendrogram	logical, should sample dendrogram plot with trait annotation be displayed?.
nThreads	numeric: number of threads to allow.
abline.threshold	numeric: height cut value in sample dendrogram used to remove offending sample(s).

Value

List object containing sample dendrogram, expression data matrix, trait data matrix and topology network plots

Examples

## Not run: 
data(DJEanlz)
SF <- system.file("extdata", "SF.expr.rds", package = "DJExpress")
SF.exp <- readRDS(SF)
colnames(DJEanlz$v.norm)[grep("TCGA", colnames(DJEanlz$v.norm))] <- paste0("TCGA_",
seq(1,length(colnames(DJEanlz$v.norm)[grep("TCGA", colnames(DJEanlz$v.norm))]), 1))
Group1 <- colnames(DJEanlz$v.norm$E)[grep("SRR", colnames(DJEanlz$v.norm$E))]
Jprep <- JCNAprepare(analize.out=DJEanlz, Group1 = Group1,
traitData = SF.exp, abline.threshold=60, input.type = "DJEanalyze.out")

## End(Not run)

MauerLab/DJExpress documentation built on Jan. 1, 2022, 12:57 p.m.