summarizeRepsNoFiltering {RNAither} | R Documentation

## Generate a new dataset with summarized replicates

### 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")

[Package RNAither version 2.36.0 Index]