TileShuffleOutput {TileShuffle} | R Documentation |
Reports the output for the exported function TileShuffle
.
TileShuffleOutput(bed, input.type, signal.filename, cel.filename, cel2.filename, celinc.filename, custom.filename, custom2.filename, custominc.filename, bpmap.filename, minhits, group, pmonly, normalize, noofperms, winsize, qvalue, gcmode, gcnum, score.function, randomize, diff, diff.variant, regions.filename, zscore.filename, output.filename, verbose)
bed |
A list , reported by TileAnalysis , with two
entries where the first one stores all information on the windows
including their z-score in case the zscore.filename is not set
to NULL while the second one keeps the information on the
segments identified as (differentially) expressed. |
input.type |
The type of input data which contains the probe and
intensity information. In case of input.type == 1 , the input
is read by use of the function TileReadSignal . On the
other hand, in case of input.type == 2 , the input is read
by using the function TileReadCel while it is read by
TileReadCustom if input.type == 3 is selected. |
signal.filename |
Filename as a character that is required by
the function TileReadSignal . |
cel.filename |
A vector of one or more filenames as
character that is required by the function
TileReadCel . |
cel2.filename |
A vector of one or more filenames as
character that is required by the function
TileReadCel if diff is enabled. |
celinc.filename |
A vector of one or more filenames as
character that may be provided to the function
TileReadCel . |
custom.filename |
A vector of one or more filenames as
character that is required by the function
TileReadCustom . |
custom2.filename |
A vector of one or more filenames as
character that is required by the function
TileReadCustom if diff is enabled. |
custominc.filename |
A vector of one or more filenames as
character that may be provided to the function
TileReadCustom . |
bpmap.filename |
Filename as a character that is required by the
function TileReadSignal and TileReadCel . |
minhits |
An integer value that is required by the function
TileReadSignal and TileReadCel . |
group |
A character value that is required by the function
TileReadSignal and TileReadCel . |
pmonly |
A logical value that may be provided to the function
TileReadCel and TileReadCustom . |
normalize |
A logical value that may be provided to the function
TileReadCel and TileReadCustom . |
noofperms |
An integer value that is required by the function
TileAnalysis . |
winsize |
An integer value that is required by the function
TileAnalysis . |
qvalue |
A numeric value that is required by the function
TileAnalysis . |
gcmode |
A character value that is required by the function
TileAnalysis . |
gcnum |
An integer value that is required by the function
TileAnalysis . |
score.function |
A character value that is required by the
function TileAnalysis . |
randomize |
A logical value that is required by the function
TileAnalysis . |
diff |
A logical value that is required by the function
TileAnalysis . |
diff.variant |
A character value that is required by the
function TileAnalysis if diff is enabled. |
regions.filename |
Filename as a character that may be provided
to to the function TileAnalysis . |
zscore.filename |
Filename as a character where the analyzed
windows by of the statistical analysis including the given
information are written to (if zscore.filename is not set
to NULL ). Note that any existing file will be overwritten. |
output.filename |
Filename as a character where the identified
segments including the given information are written to. Note that
any existing file will be overwritten. |
verbose |
A logical value. |
Reports the output for the exported function TileShuffle
as a
BED-formatted output file that is written and comprises information on the
segments identified as significantly (differentially) expressed. Moreover,
if zscore.filename
is given accordingly (not set to NULL
) an
addiional BED-formatted file is written that comprises the analyzed windows
of the statistical analysis. Note that any existing file will be overwritten.
Moreover, all generated files contain header information marked by `#' at the
beginning of the line that lists the used parameters with their values and
the description of the columns in the corresponding file.
None. All output is written to the output.filename
and
zscore.filename
if zscore.filename
is not NULL
.