create_gr_from_sample: Create GRange object from sample data frame

In popopo19/excerno: Fillter out somatic mutations generated by the Formalin-Fixed Paraffin-Embedded (FFPE) tissue preservation technique from cancer tissue

Create GRange object from sample data frame

Description

Generate a GRange object from sample data frame with additional columns for a vcf file

Usage

create_gr_from_sample(
  sample.df,
  seq,
  chromosome,
  info = c(),
  quality = c(),
  filter = c(),
  format = c(),
  samples = list(),
  sample.names = c()
)

Arguments

sample.df	A data frame with columns 'mutations' and 'truth'. See output of classify_simulated_samples() for example
seq	A DNAString. The sequence of a chromosome.
chromosome	A string of the chromosome
info	A vector for the info column
quality	A vector for the quality column
filter	A vector for the filter column
format	A vector for the format column
samples	A list of vectors for the sample columns
samples.names	A vector of strings for the sample column headers

Value

A GRange object with the information inserted

Examples

library(MutationalPatterns)
library(tidyverse)
library(Biostrings)
library(BSgenome.Hsapiens.UCSC.hg38)
library(GenomicRanges)

# Load in signatures
cosmic.sigs <- get_known_signatures()
cosmic.sig4 <- as.matrix(cosmic.sigs[,4])
ffpe.sig <- get_ffpe_signature()

# Create samples
sample.sig4 <- create_signature_sample_vector(cosmic.sig4, 100)
sample.ffpe <- create_signature_sample_vector(ffpe.sig, 100)

# Create classification data frame
samples <- list(sample.sig4, sample.ffpe)
signatures <- list(cosmic.sig4, ffpe.sig)
classify.df <- classify_simulated_samples(samples, signatures)

seq <- getSeq(Hsapiens, "chr1")

create_gr_from_sample(classify.df, seq, "chr1")

# Adding values to other columns
info <- sample("SOMATIC", 200, replace = TRUE)
quality <- sample(50:100, 200, replace = TRUE)
filter <- sample("PASS", 200, replace = TRUE)
format <- sample("GT:GQ", 200, replace = TRUE)
samples <- list(sample(paste("0/0:", 1:100, sep = ""), 200, replace = TRUE), sample(paste("0/0:", 1:100, sep = ""), 200, replace = TRUE))
sample.names <- c("SAMPLE1", "SAMPLE2")
create_gr_from_sample(classify.df, seq, "chr1", info, quality, filter, format, samples, sample.names)

popopo19/excerno documentation built on Aug. 28, 2022, 1:23 a.m.