Create the Profile GDS file(s) for one or multiple specific profiles using the information from a RDS Sample description file and the 1KG GDS file

The function uses the information for the Reference GDS file and the RDS Sample Description file to create the Profile GDS file. One Profile GDS file is created per profile. One Profile GDS file will be created for each entry present in the listProfiles parameter.

createStudy2GDS1KG(
  pathGeno = file.path("data", "sampleGeno"),
  filePedRDS = NULL,
  pedStudy = NULL,
  fileNameGDS,
  batch = 1,
  studyDF,
  listProfiles = NULL,
  pathProfileGDS = NULL,
  genoSource = c("snp-pileup", "generic", "VCF"),
  verbose = FALSE
)

Arguments

pathGeno

a character string representing the path to the directory containing the VCF output of SNP-pileup for each sample. The SNP-pileup files must be compressed (gz files) and have the name identifiers of the samples. A sample with "Name.ID" identifier would have an associated file called if genoSource is "VCF", then "Name.ID.vcf.gz", if genoSource is "generic", then "Name.ID.generic.txt.gz" if genoSource is "snp-pileup", then "Name.ID.txt.gz".

filePedRDS

a character string representing the path to the RDS file that contains the information about the sample to analyse. The RDS file must include a data.frame with those mandatory columns: "Name.ID", "Case.ID", "Sample.Type", "Diagnosis", "Source". All columns must be in character strings. The data.frame must contain the information for all the samples passed in the listSamples parameter. Only filePedRDS or pedStudy can be defined.

pedStudy

a data.frame with those mandatory columns: "Name.ID", "Case.ID", "Sample.Type", "Diagnosis", "Source". All columns must be in character strings (no factor). The data.frame must contain the information for all the samples passed in the listSamples parameter. Only filePedRDS or pedStudy can be defined.

fileNameGDS

a character string representing the file name of the Reference GDS file. The file must exist.

batch

a single positive integer representing the current identifier for the batch. Beware, this field is not stored anymore. Default: 1.

studyDF

a data.frame containing the information about the study associated to the analysed sample(s). The data.frame must have those 3 columns: "study.id", "study.desc", "study.platform". All columns must be in character strings (no factor).

listProfiles

a vector of character string corresponding to the profile identifiers that will have a Profile GDS file created. The profile identifiers must be present in the "Name.ID" column of the Profile RDS file passed to the filePedRDS parameter. If NULL, all profiles present in the filePedRDS are selected. Default: NULL.

pathProfileGDS

a character string representing the path to the directory where the Profile GDS files will be created. Default: NULL.

genoSource

a character string with two possible values: 'snp-pileup', 'generic' or 'VCF'. It specifies if the genotype files are generated by snp-pileup (Facets) or are a generic format CSV file with at least those columns: 'Chromosome', 'Position', 'Ref', 'Alt', 'Count', 'File1R' and 'File1A'. The 'Count' is the depth at the specified position; 'FileR' is the depth of the reference allele and 'File1A' is the depth of the specific alternative allele. Finally the file can be a VCF file with at least those genotype fields: GT, AD, DP.

verbose

a logical indicating if message information should be printed. Default: FALSE.

Value

The function returns 0L when successful.

Author

Pascal Belleau, Astrid Deschênes and Alexander Krasnitz

Examples

## Path to the demo 1KG GDS file is located in this package
dataDir <- system.file("extdata/tests", package="RAIDS")
fileGDS <- file.path(dataDir, "ex1_good_small_1KG.gds")

## The data.frame containing the information about the study
## The 3 mandatory columns: "study.id", "study.desc", "study.platform"
## The entries should be strings, not factors (stringsAsFactors=FALSE)
studyDF <- data.frame(study.id = "MYDATA",
                        study.desc = "Description",
                        study.platform = "PLATFORM",
                        stringsAsFactors = FALSE)

## The data.frame containing the information about the samples
## The entries should be strings, not factors (stringsAsFactors=FALSE)
samplePED <- data.frame(Name.ID=c("ex1", "ex2"),
                    Case.ID=c("Patient_h11", "Patient_h12"),
                    Diagnosis=rep("Cancer", 2),
                    Sample.Type=rep("Primary Tumor", 2),
                    Source=rep("Databank B", 2), stringsAsFactors=FALSE)
rownames(samplePED) <- samplePED$Name.ID

## Create the Profile GDS File for samples in 'listSamples' vector
## (in this case, samples "ex1")
## The Profile GDS file is created in the pathProfileGDS directory
result <- createStudy2GDS1KG(pathGeno=dataDir,
            pedStudy=samplePED, fileNameGDS=fileGDS,
            studyDF=studyDF, listProfiles=c("ex1"),
            pathProfileGDS=tempdir(),
            genoSource="snp-pileup",
            verbose=FALSE)

## The function returns OL when successful
result
#> [1] 0

## The Profile GDS file 'ex1.gds' has been created in the
## specified directory
list.files(tempdir())
#> [1] "downlit"         "ex1.gds"         "file4d2deb02dfc"

## Remove Profile GDS file (created for demo purpose)
unlink(file.path(tempdir(), "ex1.gds"), force=TRUE)