pca: generating a PCA from counts, FPKM and TPM tables from...

Description Usage Arguments Value Author(s) Examples

View source: R/pca.R

Description

This function generates PCA plot from counts, FPKM and TPM tables from rnaseqCounts outuputs.

Usage

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pca(experiment.table = "_counts.txt", type = c("counts", "FPKM",
  "TPM"), covariatesInNames = FALSE, samplesName = TRUE,
  principal.components = c(1, 2), legend.position = c("bottom",
  "bottomleft", "left", "topleft", "top", "topright", "right", "center"),
  pdf = TRUE, output.folder = getwd())

Arguments

experiment.table,

a character string indicating the counts, FPKM or TPM table file name

type,

a character value indicating the content of the file: counts, FPKM or TPM

covariatesInNames,

a boolean value indicating if covariates are inserted after \_ in the filename

samplesName,

a boolean value indicating if in the plot samples names are plotted or not

principal.components,

a numerical vector with two values indicating the principal components to be plotted

legend.position,

a character string indicating the location of the covariates legend

pdf,

a boolean value indicating if results has to be saved in a pdf

output.folder,

output folder

Value

Returns a PCA plot

Author(s)

Raffaele Calogero

Examples

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## Not run: 
  system("wget 130.192.119.59/public/test.analysis.zip")
  unzip("test.analysis.zip")
  setwd("test.analysis")
  library(docker4seq)
  pca(experiment.table="_log2FPKM.txt", type="FPKM",
      legend.position="topleft", covariatesInNames=FALSE, samplesName=TRUE,
      principal.components=c(1,2), pdf = TRUE,
      output.folder=getwd())


## End(Not run)

kendomaniac/docker4seq documentation built on Oct. 18, 2018, 11:19 p.m.