summarizeSigCounts: Summarize a contrast list

In DGEobj.utils: Differential Gene Expression (DGE) Analysis Utility Toolkit

Summarize a contrast list

Description

Takes a contrast list produced by runContrasts. Defaults are provided to specify columns to summarize and thresholds for each column, though they can be adjusted. A fold change threshold can optionally be specified. The function queries the topTable results and returns a dataframe with the summary results, but only includes gene counts that meet the specified conditions.

Usage

summarizeSigCounts(
  contrastList,
  columns = c("P.Value", "adj.P.Val", "Qvalue", "qvalue.lfdr", "ihw.adj_pvalue"),
  sigThresholds = c(0.01, 0.05, 0.05, 0.05, 0.05),
  fcThreshold = 0
)

Arguments

contrastList	A list of topTable dataframes.
columns	Vector of column names to summarize from topTable dataframes. Default = c("P.Value", "adj.P.Val", "Qvalue", "qvalue.lfdr", "ihw.adj_pvalue")
sigThresholds	Thresholds to use for each column specified in columns Must be same length at columns argument. Default = c(0.01, 0.05, 0.05, 0.05, 0.05)
fcThreshold	Fold-change threshold (absolute value, not logged.)

Details

Any specified column names that don't exist will be ignored. Normally the defaults cover all the p-value and FDR related columns. However, a fcThreshold can be added and the p-value/FDR thresholds can be modified using the fcThreshold and sigThresholds arguments, respectively.

Value

data.frame with one summary row per contrast.

Examples

   dgeObj <- readRDS(system.file("exampleObj.RDS", package = "DGEobj"))
   contrastList <- DGEobj::getType(dgeObj, type = "topTable")

   #all defaults
   sigSummary <- summarizeSigCounts(contrastList)

   #add the fold-chage threshold
   sigSummary <- summarizeSigCounts(contrastList, fcThreshold = 2)

   #change the significance thresholds
   sigSummary <- summarizeSigCounts(contrastList,
                                    sigThresholds = c(0.01, 0.1, 0.1, 0.1, 0.1))

DGEobj.utils documentation built on May 20, 2022, 1:08 a.m.