DGEobj.utils (version 1.0.6)

extractCol: Extract a named column from a series of df or matrices

Description

Take a named list of dataframes where each dataframe has the same column names (e.g. a list of topTable dataframes), then extract the named column from each dataframe and return a matrix. The name of each dataframe is used as the column name in the resulting table.

Usage

extractCol(contrastList, colName, robust = TRUE)

Arguments

contrastList

A list of data.frames which all have the same colnames and same row counts. The dataframes in the list should have geneIDs as rownames.

colName

The name of the data column to extract into a matrix.

robust

Default = TRUE; TRUE forces use of a joins to merge columns which is more reliable and allows for combination of contrasts from different projects, but may not return items in the same row order as the source table. Setting to FALSE invokes a cbind() approach that requires all data.frames to have the same row count and row order but preserves the original row order.

Value

A dataframe containing the extracted columns

Details

The common use case for this is to provide a list of topTable data frames and extract one column from each file to create a matrix of LogRatios or P-values (genes x contrasts)..

This should work as long as the requested column name is present in every dataframe. The default robust = TRUE should be used unless it has been verified that each dataframe in the input list has the same row count and row order.

Examples

# NOT RUN {
   dgeObj <- readRDS(system.file("exampleObj.RDS", package = "DGEobj"))
   TopTableList <- DGEobj::getType(dgeObj, type = "topTable")
   MyPvalues    <- extractCol(TopTableList, colName = "P.Value")
   head(MyPvalues)

# }