Description Usage Arguments Value Author(s) Examples
View source: R/callAlterations.R
This function can be used to obtain gene-level copy number calls from segmentations. This is useful for comparing PureCN's segmentations with segmentations obtained by different tools on the gene-level. Segmentation file can contain multiple samples.
1 2 3 4 5 6 7 8 9 10 11 12 13 |
sampleid |
The sampleid column in the segmentation file. |
chr |
The chromosome column. |
start |
The start positions of the segments. |
end |
The end positions of the segments. |
num.mark |
Optionally, the number of probes or markers in each segment. |
seg.mean |
The segment mean. |
C |
The segment integer copy number. |
interval.file |
A mapping file that assigns GC content and gene symbols
to each exon in the coverage files. Used for generating gene-level calls.
First column in format CHR:START-END. Second column GC content (0 to 1).
Third column gene symbol. This file is generated with the
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fun.focal |
Function for identifying focal amplifications. Defaults to
|
args.focal |
Arguments for focal amplification function. |
... |
Arguments passed to |
A list of callAlterations
data.frame
objects,
one for each sample.
Markus Riester
1 2 3 4 5 6 7 8 | data(purecn.example.output)
seg <- purecn.example.output$results[[1]]$seg
interval.file <- system.file("extdata", "example_intervals.txt",
package = "PureCN")
calls <- callAlterationsFromSegmentation(sampleid=seg$ID, chr=seg$chrom,
start=seg$loc.start, end=seg$loc.end, num.mark=seg$num.mark,
seg.mean=seg$seg.mean, C=seg$C, interval.file=interval.file)
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