read_score: Read repeat score data produced from Bio::STR::exSTRa

In bahlolab/exSTRa: Expanded STR algorithm: detecting expansions in Illumina sequencing data

Read repeat score data produced from Bio::STR::exSTRa

Description

read_score reads output from the Perl module Bio::STR::exSTRa.

Usage

read_score(
  file,
  database,
  groups.regex = NULL,
  groups.samples = NULL,
  filter.low.counts = TRUE
)

Arguments

file	Path of file to read.
database	Path of database file (character) or exstra database (exstra_db object).
groups.regex	Sets the sample groups with a regular expression. This is a named character vector of R regular expressions, where names correspond to the group and regular expressions to match the sample names. The first match in the vector takes priority over other matches, such that it may be sensible to have the final regex as the empty string: "". Group names should only be 'case', 'control' or 'null'.
groups.samples	Sets the sample groups with a named list of character vectors, with names the group and vectors of sample names. Group names should only be 'case', 'control' or 'null'.
filter.low.counts	If TRUE, apply automatic filtering of counts lower than expected by chance (assuming independent and uniform DNA base distribution).

References

Bio::STR:exSTRa Perl module https://github.com/bahlolab/Bio-STR-exSTRa

Examples

str_score <- read_score (
    file = system.file("extdata", "HiSeqXTen_WGS_PCR_2.txt", package = "exSTRa"), 
    database = system.file("extdata", "repeat_expansion_disorders_hg19.txt", package = "exSTRa"), 
    groups.regex = c(control = "^WGSrpt_0[24]$", case = ""), 
    filter.low.counts = TRUE
)
str_score
str_score$samples

# Plot the HD locus only:
plot(str_score["HD"])


# Defining cases by sample name directly:
str_score_HD_cases <- read_score (
    file = system.file("extdata", "HiSeqXTen_WGS_PCR_2.txt", package = "exSTRa"), 
    database = system.file("extdata", "repeat_expansion_disorders_hg19.txt", package = "exSTRa"),
    groups.samples = list(case = c("WGSrpt_10", "WGSrpt_12")),
    filter.low.counts = TRUE
)
str_score_HD_cases
str_score_HD_cases$samples

plot(str_score_HD_cases["HD"])

# for greater control, use object from read_exstra_db() instead
str_db <- read_exstra_db(
            system.file("extdata", "repeat_expansion_disorders_hg19.txt", package = "exSTRa")
          )
str_score <- read_score (
    file = system.file("extdata", "HiSeqXTen_WGS_PCR_2.txt", package = "exSTRa"), 
    database = str_db, 
    groups.regex = c(control = "^WGSrpt_0[24]$", case = ""), 
    filter.low.counts = TRUE
)
str_score
str_score$samples

bahlolab/exSTRa documentation built on Sept. 17, 2022, 5:08 p.m.