pca_plot_enrich: pca_plot_enrich (from pcaGoPromoter functions).
In ShirinG/exprAnalysis: A package for analysing RNA-seq and expression array data

Description Usage Arguments Details Value

This is a collection of functions from the package "pcaGoPromoter". It calculates the principle components and plots them. It also calculates TF and GO term enrichments.

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pca_plot_enrich(expmatrix, groups, PCs = c(1, 2), main = "PCA plot",
  percentage = 2.5, inputType = "geneSymbol", org = "Hs",
  projectfolder = getwd())

`expmatrix`	An input matrix with gene names as row names and sample names as column names.
`groups`	Define sample groups.
`PCs`	Principle components to plot (pick two). Defaults to PCs 1 and 2.
`main`	Main title of PCA plot. Defaults to "PCA plot".
`percentage`	Percentage of genes with top loadings to use for TF and GO enrichment analysis. Defauls to 2.5.
`inputType`	a character vector description the input type. Must be Affymetrix chip type, "geneSymbol" or "entrezID". The following Affymetrix chip type are supported: hgu133plus2, mouse4302, rat2302, hugene10st and mogene10st. Default is Affymetrix chip type "hgu133plus2".
`org`	a character vector with the organism. Can be "Hs", "Mm" or "Rn". Only needed if inputType is "geneSymbol" or "entrezID". See details. Default is "Hs".
`projectfolder`	File path where to save the tables to. Defaults to working directory. Here, it saves the output to a subfolder called "pcaGoPromoter".

Both, PC plot (as .pdf) and tables (as tab delimited .txt) of enriched TFs and GO terms are saved by default to the working directory or to the given path.

A PCA plot and tables of enriched TFs and GO terms.

ShirinG/exprAnalysis documentation built on May 9, 2019, 1:28 p.m.