R/mod-CNregions.R
CNregions.mod.Rd
CNregions.mod Modified CNregions function from the facets package to handle small sample sizes.
CNregions.mod( seg, epsilon = 0.005, adaptive = FALSE, rmCNV = FALSE, cnv = NULL, frac.overlap = 0.5, rmSmallseg = TRUE, nProbes = 15 )
seg | a segmentation file containing the segmentation information of multiple patients |
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epsilon | the maximum Euclidean distance between adjacent probes tolerated for denying a nonredundant region. epsilon=0 is equivalent to taking the union of all unique break points across the n samples. |
adaptive | Vector of length-m lasso penalty terms. |
rmCNV | If TRUE, remove germline CNV. |
cnv | A data frame containing germline CNV data. |
frac.overlap | A parameter needed to be explain. |
rmSmallseg | If TRUE, remove small segment. |
nProbes | The segment length threshold below which the segment will be removed if rmSmallseq = TRUE. |
reducedM : A matrix ready for plotting.
#> #>#>#> #>#>#> #>samples <- as.character(unique(mut$Tumor_Sample_Barcode))[ sample(1:length(unique(mut$Tumor_Sample_Barcode)), 100, replace=FALSE)] CNregions.mod(seg %>% filter(ID %in% samples))[1:5,1:5]#> chr1.2488138-11167550 chr1.11167550-14192672 #> P-0000145-T01-IM3 -0.0290 -0.0290 #> P-0000216-T02-IM3 -0.2137 -0.2137 #> P-0000231-T01-IM3 -0.0391 -0.0391 #> P-0000242-T01-IM3 -0.3706 0.0444 #> P-0000244-T01-IM3 -0.3711 -0.0041 #> chr1.14192672-16199471 chr1.16199471-17345415 #> P-0000145-T01-IM3 -0.0290 -0.0290 #> P-0000216-T02-IM3 -0.2137 -0.2137 #> P-0000231-T01-IM3 -0.0391 -0.0391 #> P-0000242-T01-IM3 0.0444 0.0444 #> P-0000244-T01-IM3 -0.0041 -0.0041 #> chr1.17345415-22587878 #> P-0000145-T01-IM3 -0.0290 #> P-0000216-T02-IM3 -0.2137 #> P-0000231-T01-IM3 -0.0391 #> P-0000242-T01-IM3 0.0444 #> P-0000244-T01-IM3 -0.0041