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"
: 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"]]
.
wellAnno
: well annotation as given by the plate configuration file.
finalWellAnno
: 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
.
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())