Barcode PCA plot

Takes a DGEList object contining barcode cpm counts and performs PCA. Then, plots the first two dimensions. Modified from DESeq2 package plotPCA function

Usage

plotBarcodePCA(
  dgeObject,
  groups = NULL,
  ntop = 500,
  returnData = FALSE,
  pcs = c(1, 2),
  batch = NULL
)

Arguments

dgeObject

DGEList object with barcode counts.

groups

Optional, one or multiple column names in sample metadata to color samples by (string or vector of strings).

ntop

number of top most variable barcodes to be used in PCA calculation (integer). Default = `500`.

returnData

Return a data.frame of PCA calculation instead of plot (boolean). Default = `FALSE`.

pcs

Principle components to plot (vector of integers of length 2). Default = `c(1, 2)`.

batch

Optional, metadata category indicating source of batch effects. Will be used in limma removeBatchEffect function prior to PCA.

Value

Returns a plot of the first two principal components in the dataset

Details

plotBarcodePCA

Plot the first two principal components of the barcode dataset

Examples

data(test.dge)
plotBarcodePCA(test.dge, groups = "Treatment", ntop = 500, returnData = FALSE, batch = NULL)