checkNegCtrlGenes: Check Unwanted variation in Negative Control Genes

In AbhishekSinha28/tcgaCleaneR: TGCA Data Analysis

Check Unwanted variation in Negative Control Genes

Description

This function is a part of the data analysis functionality of tcgaCleaneR. It helps to visualize the presence of unwanted variation in the Negative Control Genes (NCG) for RUV-III analysis. Using PCA analysis any relation between the negative control sets in the TCGA data and the unwanted variation type can be visualized. The plot between PCs and unwanted variation can help verify the presence of unwanted variation in NCG sets.

Usage

checkNegCtrlGenes(data, ncg_set, group, plot_type, nPcs, npcs, is.log)

Arguments

data	S4 data object
ncg_set	character: A character vector of NCG sets from TCGA data. At present TCGA data includes the following NCG variables i.e. "scRNAseq_HK","RNAseq_HK","Microrray_HK","NanostringPanCancer_HK" and "sinscorePanCancer_HK".
group	character: Color code PCs based on group. groups included are 'Time', 'Tissue', 'Plate', 'TSS', 'Center'
plot_type	character: Plot type. Includes 'DensityPlot' and 'BoxPlot'.
nPcs	numeric: Number of PCs that needs to be computed
npcs	numeric: Number of PCs that needs to be plotted
is.log	logical: Checks if the S4 data has log values. If 'False', it converts data to log scale.

Value

Density Plot, Box Plot

Examples

## Not run: 
checkNegCtrlGenes(data =brca.data, ncg_set= c("Microrray_HK"), group='Time', plot_type="DensityPlot", nPcs=10, npcs = 3, is.log=FALSE)
checkNegCtrlGenes(data =brca.data, ncg_set= c("Microrray_HK","scRNAseq_HK"), group='Tissue', plot_type="BoxPlot", nPcs=7, npcs = 2, is.log=FALSE)

## End(Not run)

AbhishekSinha28/tcgaCleaneR documentation built on May 6, 2022, 6:46 a.m.