JCNAgenePrepare: JCNAGenePrepare: WGCNA annotation for junction expression...

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

Description

Performs weighted junction co-expression network analysis using gene expression and returns output object for JCNA2pass.

Usage

JCNAgenePrepare(
  pass1.out,
  genExpr,
  Group1 = NULL,
  gtf,
  nThreads = 2,
  abline.threshold = NULL,
  networkType = "unsigned",
  level = 0.95,
  cor.method = c("bicor", "pearson", "kendall", "spearman")
)

Arguments

pass1.out	output object from JCNA1pass()
genExpr	Gene expression data. A matrix (preferred) or data frame in which columns are genes and rows ar samples. NAs are allowed, but not too many. See WGCNA::checkMissingData and details.
Group1	vector or factor specifying basic control sample names
gtf	Reference transcriptome in a gtf file. Used to define gene identity of junctions
nThreads	numeric: number of threads to allow.
abline.threshold	numeric: height cut value in sample dendrogram used to remove offending sample(s)
networkType	network type. Allowed values are (unique abbreviations of) "unsigned", "signed", "signed hybrid". See adjacency.
level	numeric: confidence interval for Linear Regression of Junction vs Gene trait association value
cor.method	a character string specifying the method to be used for correlation as in WGCNA. Options are "bicor", "pearson", "kendall" or "spearman".

Value

A list object containing: Gene.sampletree: Sample dendrogram based on gene expression Gene.hc: Sample dendrogram with trait heatmap Gene.NetTop: Analysis of network topology for various soft-thresholding powers produced by pickSoftThreshold in WGCNA. Left panel shows scale-free fit index (y-axis) as a function of the soft-thresholding power (x-axis). The right panel displays mean connectivity (degree, y-axis) as a function of the soft-thresholding power (x-axis). Gene.net: Constructed gene network and detected modules using blockwiseModules from WGCNA Gene.ModuleTrait: Heatmap with Gene Modules vs Trait associations Genetrait: Data frame with correlation coefficients and associated P-values (Gene expression vs traits) GeneToJunct: Data frame with junction coordinates and correspondent gene JunctGeneTrait: List of data frames with integrated information about junction and gene associations per trait

Examples

## Not run: 
gtf0 <- system.file("extdata", "chr1.gtf.gz", package = "DJExpress")
gexp <- system.file("extdata", "genExpr.rds", package = "DJExpress")
filgenExpr <- readRDS(gexp)
J1pass0 <- system.file("extdata", "J1pass.rds", package = "DJExpress")
J1pass <- readRDS(J1pass0)
JgPrep <- JCNAgenePrepare(pass1.out = J1pass, genExpr = filgenExpr,
                          gtf=gtf0, networkType = "unsigned", cor.method = "bicor")

## End(Not run)

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