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

In kendomaniac/docker4seq: Running NGS computing demanding applications, e.g reads mapping and counting, wrapped in docker containers

generating a PCA from counts, FPKM and TPM tables from rnaseqCounts outuputs

Description

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

Usage

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 and its path
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

## 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 Sept. 3, 2024, 6:42 p.m.