Description Usage Arguments Details Value Author(s) Examples
Match the ChIP files with input files.
1 | ChIPInputMatch(dir, suffices, depth = 5, celltypes)
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dir |
A string vector of length 2. The first entry is the ChIP file directory and the second is the input file directory. It is required that ChIP and input files must be in two different directories. |
suffices |
A vector of strings for the suffices of each file name. |
depth |
The maximum depth under the dir paths that the files are stored. Default: 5. |
This function matches the ChIP files with the control files according to their filenames. The file names must follow the ENCODE consortium convention, i.e. the prefix of the file name is wgEncode<lab><experiment_type><cellline><factor><control>Aln[replicate]. Each string in <.> must has one single initial capital letter followed by lower case letters or digits.
A data.frame object with the following fields:
chipfile | The name of the ChIP file. |
inputfile | The prefix of the matching input files (i.e. without replicate identifiers). |
lab | The string for the lab information. |
experiment | The string for the experiment type. |
cellline | The string for the cellline. |
factor | The string for the factor. |
control | The string for the control experiment. |
chiptype | The file format of the ChIP data. |
inputtype | The file format of the input data. |
Chandler Zuo zuo@stat.wisc.edu
1 | ## Not run: ChIPInputMatch(c("ChIPDataDir/", "inputDataDir/"), suffices = ".tagAlign", depth = 2)
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