summarizeSigCounts {DGEobj.utils} | R Documentation |
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))