Description Usage Arguments Details Value Author(s) See Also Examples
The function is a wrapper for getSegChr()
, which calculates the folded BAF and logR ratios for each chromosome.
1 2 3 |
BAFfilePath |
character string, full path to directory where all BAF files are located. |
logRfilePath |
character string, full path to directory where all LRR files are located. |
sam.col |
the index of the column in BAF or LRR files where the first sample starts. |
control |
If TRUE, each tumor sample is paired with normal immediately after it. The columns of the data file is organized : sample_1, control_1, sample_2, control_2 .... If FALSE, each sample serves the control of itself. |
thr.hets |
lower threshold of calling homozygous markers. BAF<=thr.hets or BAF>=1-thr.hets are considered homozygous. |
bin |
integer, number of markers in each bin. |
savefile |
character string, Rdata file to be saved in working directory. |
data.type |
character string chosen from c('copy', 'log'). If 'copy', the value for LRR markers represent the copy number of SNPs. If 'log', the value is log2 based copy number intensity. |
cbs |
if TRUE, circular binary segmentation will be performed using R package 'DNAcopy', instead of binned segmentation. |
controlOne |
default 0. If assigned, must be an integer number indicating the index of one control sample in the sample list. This control will be used for all the samples. |
nt |
logical. If true, multi-thread processing is applied. This option is system dependent. |
The input format for BAF and LRR files are the same and as follows: 1) in the directory, there are n tab-deliminated plain text files, where n is the number of chromosomes, with file name chrN.txt, N=1,2,...22. sex and mitochondria chromosomes are currently not included in the analysis. No other file should be included. 2) for tumor/normal paired design (control
=TRUE), each plain text file must have the following fields:
Marker-ID, chromosome, start position, end position, Tumor 1, Paired-normal 1, Tumor 2, Paired-normal 2, ..., etc. For study with tumors matched with one control sample, the order of samples is not required.
It is not necessary to sort the genomic positions beforehand.
NULL. An Rdata file with variable name 'dd.dat' will be saved in the working directory with following fields: sample-ID, chromosome, start position, end position, LRR value, number of LRR markers, BAF value, number of BAF markers. The saved file can be immediately used in downstream analysis.
Bo Li
1 2 3 4 | ## Not run:
getSeg(directory_to_BAF_files, directory_to_LRR_files, bin=1000)
## End(Not run)
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