DGEobj.utils (version 1.0.6)

summarizeSigCounts: 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.)

Value

data.frame with one summary row per contrast.

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.

Examples

# NOT RUN {
   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))

# }