deconstrucsSigs data example

Load libraries

library(dplyr)
library(magrittr)
library(deconstructSigs)

Load data

example_data <- sample.mut.ref # Example from package
jasmine_data <- read.csv("forbreastsdeconsctructSigsSNV.txt", sep = "\t")

The diffrences

example_data %>% names()

[1] "Sample" "chr"    "pos"    "ref"    "alt"   

jasmine_data %>% names()

[1] "sample.id" "chr"       "pos"       "ref"       "alt"      

• The name of the first column should be "Sample" and not "sample.id".

example_data %>% filter(is.na(chr)) %>% nrow()

[1] 0

jasmine_data %>% filter(is.na(chr)) %>% nrow()

[1] 833

• NAs aren’t allowed in the data.

example_data %>% select(chr) %>% head()

   chr
1 chr1
2 chr1
3 chr1
4 chr1
5 chr1
6 chr1

jasmine_data %>% select(chr) %>% head()

  chr
1   1
2   1
3   1
4   1
5   1
6   1

• Chromosome values should start with chr.

Fix the problems

names(jasmine_data)[1] <-  "Sample"
jasmine_data %<>% filter(!is.na(chr))
jasmine_data$chr <- paste0("chr", jasmine_data$chr)

Detect signatures

sigs.input <- mut.to.sigs.input(jasmine_data)
sigs.input %>% rmarkdown::paged_table()

plot_example <- whichSignatures(sigs.input, sample.id = "NA4", contexts.needed = T)
plotSignatures(plot_example)

makePie(plot_example)