getTopTable: Generate the hit list from a scored cellHTS object

In cellHTS2: Analysis of cell-based screens - revised version of cellHTS

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().

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:

"raw":

a cellHTS object containing unpreprocessed data. I.e. state(cellHTSlist[["raw"]])["normalized"]=FALSE.

"normalized":

a cellHTS object containing normalized data. I.e. state(cellHTSlist[["normalized"]])["normalized"]=TRUE and state(cellHTSlist[["normalized"]])["scored"]=FALSE.

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):

plate:

plate identifier for each well.

position:

gives the position of the well in the plate (ranges from 1 to the total number of wells in the plate).

well:

gives the alphanumeric identifier for the wells.

score:

content of slot assayData of the scored cellHTS object given in cellHTSlist[["scored"]].

codewellAnno:

ell annotation as given by the plate configuration file.

codefinalWellAnno:

gives the final well annotation for the scored values. It combines the information given in the plate configuration file with the values in assayData slot of the scored cellHTS object, in order to have into account the wells that have been flagged either by the screen log file, or manually by the user during the analysis. These flagged wells appear with the annotation flagged.

raw_ri_chj:

(if cellHTSlist[["raw"]] is given) contains the raw intensities for replicate i in channel j (content of slot assayData of the cellHTS object given in cellHTSlist[["raw"]]).

median_chj:

(if cellHTSlist[["raw"]] is given) corresponds to the median of raw measurements across replicates in channel j.

diff_chj:

(if cellHTSlist[["raw"]] is given and if there are two replicates or samples) gives the difference between replicate (sample) raw measurements in channel j.

average_chj:

(if cellHTSlist[["raw"]] is given and if there are more than 2 replicates or samples) corresponds to the average between replicate raw intensities for channel j.

raw/PlateMedian_ri_chj:

(if cellHTSlist[["raw"]] is given) this column gives the ratio between each raw measurement and the median intensity in each plate for replicate (or sample) i in channel j. The plate median is determined for the raw intensities using exclusively the wells annotated as sample.

normalized_ri_chj:

(if cellHTSlist[["normalized"]] is given) gives the normalized intensities for replicate (sample) i in channel j. This corresponds to the content of slot assayData of the cellHTS object given in cellHTSlist[["normalized"]].

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

Value

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

Author(s)

Ligia P. Bras [e-mail]

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())

cellHTS2 documentation built on Nov. 8, 2020, 6 p.m.