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Import LRR and BAF from text files used in the CNV analysis

Source: R/pheno_assoc.R
importLrrBaf.Rd

This function imports the LRR/BAF values and create a node for each one in the GDS file at the working folder 'Inputs' created by the setupCnvGWAS function. Once imported, the LRR values can be used to perform a GWAS directly as an alternative to copy number dosage

Usage

importLrrBaf(
  all.paths,
  path.files,
  list.of.files,
  gds.file = NULL,
  verbose = TRUE
)

Arguments

all.paths

Object returned from CreateFolderTree function with the working folder tree

path.files

Folder containing the input CNV files used for the CNV calling (i.e. one text file with 5 collumns for each sample). Columns should contain (i) probe name, (ii) Chromosome, (iii) Position, (iv) LRR, and (v) BAF.

list.of.files

Data-frame with two columns where the (i) is the file name with signals and (ii) is the correspondent name of the sample in the gds file

gds.file

Path to the GDS file which contains nodes harboring respective LRR and BAF values. The ‘snp.rs.id’, ‘sample.id’, ‘LRR’ and ‘BAF’ nodes are mandatory. Both the SNPs and samples should follow the order and length in the CNV.gds (located at all.paths["Inputs"] folder). ‘path.files’ and ‘list.of.files’ will be ignored if ‘gds.file’ is not NULL

verbose

Print the samples while importing

Value

Writes to the specified GDS file by side effect.

Author

Vinicius Henrique da Silva

Examples


# Load phenotype-CNV information
data.dir <- system.file("extdata", package="CNVRanger")

phen.loc <- file.path(data.dir, "Pheno.txt")
cnv.out.loc <- file.path(data.dir, "CNVOut.txt")
map.loc <- file.path(data.dir, "MapPenn.txt")

phen.info <- setupCnvGWAS('Example', phen.loc, cnv.out.loc, map.loc)

# Extract path names
all.paths <- phen.info$all.paths

# List files to import LRR/BAF 
list.of.files <- list.files(path=data.dir, pattern="cnv.txt.adjusted$")
list.of.files <- as.data.frame(list.of.files)
colnames(list.of.files)[1] <- "file.names"
list.of.files$sample.names <- sub(".cnv.txt.adjusted$", "", list.of.files$file.names)

# All missing samples will have LRR = '0' and BAF = '0.5' in all SNPs listed in the GDS file
importLrrBaf(all.paths, data.dir, list.of.files)
#> Warning: list.of.files has different length of the list of samples from gds
#> Start parallel import of LRR/BAF values

# Read the GDS to check if the LRR/BAF nodes were added
cnv.gds <- file.path(all.paths["Inputs"], 'CNV.gds')    
genofile <- SNPRelate::snpgdsOpen(cnv.gds, allow.fork=TRUE, readonly=FALSE)
SNPRelate::snpgdsClose(genofile)