summarizeRepsNoFiltering {RNAither} | R Documentation |
Generates a new dataset with summarized replicates. Keeps wells/spots with SpotType
-1 in the dataset, but intensity values are replaced with NA
.
summarizeRepsNoFiltering(data, funSum, col4val, col4anno, cols2del)
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" |
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
.
Returns the summarized dataset.
summarizeReps
, eraseDataSetColumn
, generateReplicateMat
, generateRepMatNoFilter
, mean
, median
, rms
, trim
, max
, min
, closestToZero
, furthestFromZero
data(exampleDataset, package="RNAither") colname4val <- c("SigIntensity", "Background", "NbCells", "PercCells") summarizeddataset <- summarizeRepsNoFiltering(dataset, mean, colname4val, "GeneName", "SDSIntensity")