comparePrep: Function comparePrep

In jrthompson54/DGE.Tools2: A function library to facilitate Differential Gene Expression Analysis

Description

Takes two topTable dataframes and outputs a dataframe suitable for function comparePlot (2 columns of LogRatio data and 2 columns of significant measures). Filter the two topTable to contain just the intersecting genes (present in both datasets). The two dataframes must have the same type of gene IDs as rownames.

Usage

comparePrep(ttList, valueCol = "logFC", significanceCol = "P.Value")

Arguments

ttList	A named list of 2 topTable dataframes (required). The names are used as column names for the value columns in the output.
valueCol	Name of column containing values to plot (default = "logFC")
significanceCol	Name of column to use for significance (default = "P.Value")

Value

A data frame with 2 LogRatio measurements and 2 significance columns. Columns 1 and 3 map to sample 1 and columns 2 and 4 map to sample 2. The returned dataframe is formatted as expected by the comparePlot function.

Examples

  #Retrieve the 1st two contrasts from a DGEobj
  ttList <- getType(dgeObj, "topTable")[1:2]

  #capture the default logFC and P.Value
  compareDat <- comparePrep(ttList)

  #switch to an FDR value for the significance measure
  compareDat <- comparePrep(ttList, significanceCol="adj.P.Val")

  #draw the plot
  cPlot <- comparePlot(compareDat)

jrthompson54/DGE.Tools2 documentation built on May 12, 2021, 8:47 p.m.