pcaExperiment {ORFik}R Documentation

Simple PCA analysis

Description

Detect outlier libraries with PCA analysis. Will output PCA plot of PCA component 1 (x-axis) vs PCA component 2 (y-axis) for each library (colored by library), shape by replicate. Will be extended to allow batch correction in the future.

Usage

pcaExperiment(
  df,
  output.dir = NULL,
  table = countTable(df, "cds", type = "fpkm"),
  title = "CDS fpkm (All genes)",
  plot.ext = ".pdf"
)

Arguments

df

an ORFik experiment

output.dir

default NULL, else character path to directory. File saved as "PCAplot_(experiment name)(plot.ext)"

table

data.table, default countTable(df, "cds", type = "fpkm"), a data.table of counts per column (default normalized fpkm values).

title

character, default "CDS fpkm (All genes)".

plot.ext

character, default: ".pdf". Alternatives: ".png" or ".jpg". Note that in pdf format the complex correlation plots become very slow to load!

Value

ggplot or invisible(NULL) if output.dir is defined or < 3 samples


[Package ORFik version 1.13.14 Index]