summarizeRepsNoFiltering: Generate a new dataset with summarized replicates

In RNAither: Statistical analysis of high-throughput RNAi screens

Description

Generates a new dataset with summarized replicates. Keeps wells/spots with SpotType -1 in the dataset, but intensity values are replaced with NA.

Usage

summarizeRepsNoFiltering(data, funSum, col4val, col4anno, cols2del)

Arguments

data	an R data frame generated with generateDatasetFile
funSum	a function used to summarize the values of a replicate, e.g. mean, median, rms, trim, max, min, closestToZero, furthestFromZero, ...
col4val	a character vector (containing for example "SigIntensity", Background, NbCells, PercCells, ...) specifying the columns that will be summarized by funSum
col4anno	a character string specifying the name of the dataset column to be used to define the replicate, e.g. "GeneName" or "Internal_GeneID"
cols2del	a character vector containing the columns to delete, for example "SDSIntensity"

Details

All columns containing replicate values will be summarized by funSum. For all columns containing positions, screen numbers, plate numbers, etc., all information for different replicates will be kept, comma-separated. All columns containing standard deviations of channels should be specified in colnames2delete.

Value

Returns the summarized dataset.

See Also

summarizeReps, eraseDataSetColumn, generateReplicateMat, generateRepMatNoFilter, mean, median, rms, trim, max, min, closestToZero, furthestFromZero

Examples

data(exampleDataset, package="RNAither")

colname4val <- c("SigIntensity", "Background", "NbCells", "PercCells")
summarizeddataset <- summarizeRepsNoFiltering(dataset, mean, colname4val, "GeneName", "SDSIntensity")

RNAither documentation built on Nov. 8, 2020, 8:06 p.m.