cellHTS (version 1.42.0)

getTopTable: Generate the hit list from a scored cellHTS object

Description

Generate the hit list from a scored cellHTS object and write it to a tab-delimited file.

Usage

getTopTable(cellHTSlist, file="topTable.txt", verbose=interactive())

Arguments

cellHTSlist

a list of cellHTS objects. See details.

file

the name of the output file. Default is "topTable.txt".

verbose

a logical value, if TRUE, the function reports its progress. Defaults to the state of interactive().

Value

• Generates the file with the hit list and outputs a data.frame with the same contents.

Details

Argument cellHTSlist should be a list containing at least one component named "scored" which corresponds to a scored cellHTS object. Other possible components of cellHTSlist can be: [object Object],[object Object] All of the components of cellHTSlist should be cellHTS objects containing data from the same experiment, but in different preprocessing stages.

This function generates a data.frame that is written to file. This data.frame and the output file contain the list of scored probes ordered by decreasing score values. They have one row for each well and plate, and contain the following columns (depending on the components of cellHTSlist):

[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object] Additionally, if the cellHTS object given in cellHTSlist[["scored"]] is already annotated, the output topTable also contains the gene annotation stored in slot featureData.

References

Boutros, M., Bras, L.P. and Huber, W. (2006) Analysis of cell-based RNAi screens, Genome Biology 7, R66.

See Also

cellHTS

Examples

data(KcViabSmall)
    xn <- normalizePlates(KcViabSmall, scale="multiplicative", log=FALSE, method="median", varianceAdjust="none") 
    xsc <- scoreReplicates(xn, sign="-", method="zscore")
    xsc <- summarizeReplicates(xsc, summary="mean")
    out <- getTopTable(cellHTSlist=list("raw"=KcViabSmall, "normalized"=xn, "scored"=xsc), file=tempfile())