Check a pedigree file

Given a pedigree file path the function attempts to load it and compare it to the reference profiles to detect possible errors.

Usage

checkPedigreeFile(filename, df)

Arguments

filename

Path of the pedigree file

df

Data frame with reference profiles

Value

A list containing

• df A list of class [Familias::FamiliasPedigree()], or NULL if errors are present.

• warning A list of strings describing the errors that ocurred but could be fixed or that do not prevent the execution of the program.

• error A list of strings describing the errors that ocurred that made it imposible to return a valid data frame. If this list is not empty, then the dataframe item will be null.

Details

The pedigree file must be a a text file in ped format (see the relMix vignette for an example). The data frame with reference data is used to compare names of individuals and detect possible misspellings. If warnings are found, the function attempts to fix them and explains what it has done in the warning messages. If an error is found, checking stops. The error is described in the error messages.

Author

Elias Hernandis

Examples

#First load mixture file
mixfile <- system.file("extdata","mixture_silent_ex.txt",package="relMix")
mix <- checkMixtureFile(mixfile);
#Load reference file
reffile <- system.file("extdata","references_silent.txt",package="relMix")
ref <- checkReferenceFile(reffile, mix$df)
#Check pedigree file
pedfile <- system.file("extdata","custom_pedigree_maternity_duo.ped",package="relMix")
checkPedigreeFile(pedfile,ref$df);
#> Pedigree file C:/R/library/relMix/extdata/custom_pedigree_maternity_duo.ped is imported
#> $df
#> $id
#>   C1   C2 
#> "C1" "C2" 
#> 
#> $findex
#> [1] 0 0
#> 
#> $mindex
#> [1] 0 1
#> 
#> $sex
#> [1] "female" "male"  
#> 
#> attr(,"class")
#> [1] "FamiliasPedigree"
#> 
#> $warning
#> NULL
#> 
#> $error
#> NULL
#>