wgcnaPipeline: Pipeline of WGCNA

In fanqiang1024/wgcnaPipeline: Exploit GEO dataset to carry out WGCNA and Enrichment analysis step by step.

Description

Using Gene expression data in GEO database with clinical traits to figure out the co-expression network associated with the initiation and development of diseases.

Usage

wgcnaPipeline(GeneMatrix ,probeAnnotation ,traits,method=mean,sftEstimate=20)

Arguments

GeneMatrix	GEO dataset must be Provided.Columns of gene expression matrix are Samples, and rows are ProbeID. And so for the parament only support GEO dataset
probeAnnotation	Including 2 clomuns.The first one is ProbeID, which can be matched with rownames of GeneMatrix;and the second one is definitely offical gene Symbol.
traits	The features of Samples in GeneMatrix.And also includes 1-N columns.The first one is the names of Samples which must be consistent with the columns of GeneMatrix;and the rest of columns include the Features or Traits.
method	The duplicated genes names frequently occures in the GeneMatrix. Therefroe, it's necessary to chose the method including "median" or "mean" of those genes to dealt with them. The mean, means to average those genes expression; while, the median refers to replace them with median of those genes expression.
sftEstimate	The default soft threshold, when there no suitable threshold.

References

Langfelder P, Horvath S (2008) WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 2008, 9:559 \n G Yu, LG Wang, Y Han, QY He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology 2012, 16(5):284-287

Examples

wgcnaPipeline(GeneMatrix = "GSE_series_matrix.txt.gz",probeAnnotation = "probe_annotation.tsv",traits = "numeric_labels.csv")

fanqiang1024/wgcnaPipeline documentation built on Sept. 21, 2020, 12:03 a.m.