segSummarize: Summarize CBS segmentation results

In PoisonAlien/maftools: Summarize, Analyze and Visualize MAF Files

Summarize CBS segmentation results

Description

Summarize CBS segmentation results

Usage

segSummarize(
  seg = NULL,
  build = "hg19",
  cytoband = NULL,
  thr = 0.3,
  verbose = TRUE,
  maf = NULL,
  genes = NULL,
  topanno = NULL,
  topannocols = NA
)

Arguments

seg	segmentation results generated from DNAcopy package segment. Input should be a multi-sample segmentation file or a data.frame. First six columns should correspond to sample name, chromosome, start, end, Num_Probes, Segment_Mean in log2 scale. (default output format from DNAcopy)
build	genome build. Default hg19. Can be hg19, hg38. If other than these, use 'cytoband' argument
cytoband	cytoband data from UCSC genome browser. Only needed if 'build' is other than 'hg19' or 'hg38'
thr	threshold to call amplification and deletion. Any cytobands or chromosomal arms with median logR above or below this will be called. Default 0.3
verbose	Default TRUE
maf	optional MAF
genes	Add mutation status of these genes as an annotation to the heatmap
topanno	annotation for each sample. This is passed as an input to 'annotation_col' of 'pheatmap'
topannocols	annotation cols for 'topanno'. This is passed as an input to 'annotation_colors' of 'pheatmap'

Details

A handy function to summarize CBS segmentation results. Takes segmentation results generated by DNAcopy package segment and summarizes the CN for each cytoband and chromosomal arms.

Value

List of median CN values for each cytoband and chromosomal arm along with the plotting matrix

Examples

laml.seg <- system.file("extdata", "LAML_CBS_segments.tsv.gz", package = "maftools")
segSummarize(seg = laml.seg)

#Heighlight some genes as annotation
laml.maf = system.file("extdata", "tcga_laml.maf.gz", package = "maftools") #MAF file
laml.clin = system.file('extdata', 'tcga_laml_annot.tsv', package = 'maftools') #clinical data
laml = read.maf(maf = laml.maf, clinicalData = laml.clin)

segSummarize(seg = laml.seg, maf = laml, genes = c("FLT3", "DNMT3A"))

PoisonAlien/maftools documentation built on Nov. 5, 2024, 4:12 p.m.