TileShuffleOutput {TileShuffle}R Documentation

TileShuffleOutput

Description

Reports the output for the exported function TileShuffle.

Usage

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)

Arguments

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.

Details

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.

Value

None. All output is written to the output.filename and zscore.filename if zscore.filename is not NULL.


[Package TileShuffle version 0.1.0 Index]