Description Usage Arguments Value Author(s) See Also Examples
View source: R/getSegChr.CBS.R
This function performs CBS on B-allele freqeuncies and logR ratios on one chromosome for all the samples and returns merged break points generated by the two datasets.
1 2 3 | getSegChr.CBS(bb.chr = NULL, ll.chr = NULL, sam.col=5,
control=TRUE, thr.hets=0.1, data.type = 'copy',
controlOne=0,nt=FALSE)
|
bb.chr |
numeric matrix, original B-allele frequency for a given chromosome for all samples. |
ll.chr |
numeric matrix, original logR ratio for a given chromosome for all samples. |
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. |
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. |
controlOne |
default NA. 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 |
logic, if TRUE, multi-thread processing will be used. Require R package |
a matrix containing the following columns: chromosome, start position, end position, median LRR value, number of LRR markers, folded BAF value, number of germline heterozygous BAF markers, with row names being sample ID.
Bo Li
1 2 3 4 5 6 7 |
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