PALMO (version 0.1.2)

cvCalcBulk: cvCalcBulk Function

Description

This function allows to calculate Intra-donor variations in bulk data over longitudinal timepoints. The coefficient of variation (CV=SD/mean) is calculated in Bulk data in same donor/participant across timepoints.

Usage

cvCalcBulk(
  data_object,
  meanThreshold = 1,
  cvThreshold = 5,
  median_cvThreshold = NULL,
  donorThreshold = NULL,
  housekeeping_genes = NULL,
  naThreshold = 1,
  plot_log10 = FALSE,
  selectedFeatures = NULL,
  median_cv_max = NULL,
  plotWidth = 5,
  plotHeight = 8,
  fileName = NULL,
  filePATH = NULL
)

Value

PALMO object with CV list

Arguments

data_object

Input PALMO S4 object. Contains annotation table and expression matrix or data frame. Rows represent gene/proteins column represents participant samples (same as annotation table Sample column)

meanThreshold

Average expression threshold to filter lowly expressed genes Default is 1 (log2 scale)

cvThreshold

Coefficient of variation threshold to select variable and stable genes. Default is 5 for bulk data. Users can use 10-20 for single cell average expression data.

median_cvThreshold

Optional, median of CVs from each donor/participant calculated. Threshold used to differentiate variable and stable features across donors/participants. Default, same as cvThreshold.

donorThreshold

Donor threshold number to be used, Default is number of participants

housekeeping_genes

Optional, vector of housekeeping genes. Default is c("ACTB", "GAPDH")

naThreshold

Optional, For a give feature % of donors/participants showing non-NA CVs (NAs appear due to expression ~0 or absent). Default is 1 means all donors/participants to consider. 0.5 means from 4 donors atleast 2 donors should have non-NA CVs for a given feature.

plot_log10

Optional, Plot CV vs Mean on log10 scale. Default FALSE

selectedFeatures

Optional, focus on selected genes/features.

median_cv_max

Optional, Remove features with greater than median CV Default is NULL

plotWidth

Optional, heat plot width 5 in

plotHeight

Optional, heat plot height 8 in

fileName

User-defined file name, Default outputFile

filePATH

User-defined output directory PATH Default, current directory

Examples

if (FALSE) {
palmo_obj=cvCalcBulk(data_object=palmo_obj, meanThreshold=0.1, cvThreshold=5)
}