Description Usage Arguments Details Value Author(s) See Also Examples
This is used to control the read of a meta file containing names of data files, merge, and give usable output for the main program
1 | readInput(inputFilename, formatName="Chiang", sep = "\t")
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inputFilename |
The name of file, containing relevant information of all input files |
formatName |
The format in which the data files are written in. We use the simple 'Chiang' as default format of input. |
sep |
Delimiter of the meta input file, default is tab-delimited |
The meta input file should be organized in a table format with 2 columns, one of which is 'file' and the other is 'type', indicating the data file names and whether the data is from normal or tumor. We recommend using the 'Chiang' format, as used by the datasets of Chiang (2009). This format requires minimal memory and contains all relevant information for this program. It is a table with two columns, first being the chromosome of the mapped read, and the second being the position of the read in the chromosome. One line for each observation.
normalSeq |
A list containing the combined normal/control reads |
tumorSeq |
A list containing the combined case/tumor reads |
Jeremy J. Shen
1 2 3 4 5 6 7 | # This shows the format of the meta file
data(JSSim_Meta)
print(JSSim_Meta)
# This shows the recommended format, the Chiang data format
data(JSSim_NormalSim1)
print(head(JSSim_NormalSim1))
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