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
)

Arguments

seg

a segmentation file containing the segmentation information of multiple patients

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.

Value

reducedM : A matrix ready for plotting.

Examples

#> #> Attaching package: ‘dplyr’
#> The following objects are masked from ‘package:stats’: #> #> filter, lag
#> The following objects are masked from ‘package:base’: #> #> intersect, setdiff, setequal, union
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