ploidetect: Runs Ploidetect on read count and allele frequency data

In lculibrk/Ploidetect-package: Interpretable detection of tumour purity, ploidy, copy number variation and loss of heterozygosity

Description

Runs Ploidetect on read count and allele frequency data

Usage

ploidetect(all_data, normal = 2, tumour = 1, avg_allele_freq = 3,
  window_id = 4, window_size = 5, GC = 6, plots = F, verbose = F,
  lowest = NA, comp = NA, cndiff = NA,
  segmentation_threshold = 0.75, CNA_call = F, debugPlots = F)

Arguments

all_data	input data, formatted as a data.frame where each row is a genomic bin. Columns correspond to somatic read counts, normal read counts, allele frequencies, window id (in the format chr_pos), window size, and GC content
normal	column index of normal read depth
tumour	column index of tumour read depth
avg_allele_freq	column index of snp allele frequencies in the tumour
window_id	column index of window id (formatted as chr_pos)
window_size	column index for size of the genomic bin in bp
GC	column index of GC content as a percentage
plots	Logical. should plots be output?
verbose	Logical. Print verbose messages?
lowest	Integer from 0-2. Optional. Forces the copy number identity of the lowest fit peak in the read depth KDE
comp	Integer. Forces selection of a specific comparator peak in the read depth kernel density estimate (KDE) for tumour content modeling
cndiff	Integer. Forces the copy number difference between tallest peak in read depth KDE and the peak selected in comp
segmentation_threshold	Float between 0 and 1. Threshold for segmentation of adjacent bins during copy number calling. Default is 0.75. Smaller values will produce more segments, but may result in over-segmentation of copy number data.
CNA_call	Logical. Should copy number calling be performed?
debugplots	Logical. Should plots of data normalization be output?

Value

A named list, containing three elements: TC_calls: A data.frame containing all models considered for modeling tumour purity and ploidy plots: a list of plots. Plot 1 is always a scatter plot where the x-axis is window size, y-axis is corrected somatic read counts, and points are colored by SNP allele frequency. Plot 2 shows the KDE of the data, with all peaks shown. Next, the models in TC_calls are plotted, one plot per model. Finally, if CNA_call was TRUE, copy number data is plotted, one plot per chromosome. CNA_calls: a data.frame containing segmented copy number and LOH calls

Examples

## Run Ploidetect without specifying a model
ploidetect(all_data)
## Run Ploidetect and force a model which fits the second most common copy number as being a true integer copy number 
## with copy number equal to Ploidy +- 1, and the lowest common copy number being homozygous deletion
ploidetect(all_data, comp = 2, cndiff = 1, lowest = 0)
## Run Ploidetect with the above model and also output copy number data
ploidetect(all_data, comp = 2, cndiff = 1, lowest = 0, CNA_call = T)
## Run Ploidetect with a custom segmentation_threshold 
ploidetect(all_data, comp = 2, cndiff = 1, lowest = 0, CNA_call = T, segmentation_threshold = 0.5)

lculibrk/Ploidetect-package documentation built on July 21, 2019, 3:17 a.m.