getTopTable {cellHTS2} | R Documentation |
Generate the hit list from a scored cellHTS
object and write it to a tab-delimited file.
getTopTable(cellHTSlist, file="topTable.txt", verbose=interactive())
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() . |
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"
:cellHTS
object containing unpreprocessed
data. I.e. state(cellHTSlist[["raw"]])["normalized"]=FALSE
."normalized"
: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
:position
:well
:score
:assayData
of the scored
cellHTS
object given in
cellHTSlist[["scored"]]
.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
: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
:cellHTSlist[["raw"]]
is given)
corresponds to the median of raw measurements across replicates in
channel j
.diff_chj
: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
: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
: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
: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
.
Generates the file with the hit list and outputs a
data.frame
with the same contents.
Ligia P. Bras ligia@ebi.ac.uk
Boutros, M., Bras, L.P. and Huber, W. (2006) Analysis of cell-based RNAi screens, Genome Biology 7, R66.
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())