solar2multic: Convert SOLAR-formatted output into multic-formatted...

Description Usage Arguments Side Effects See Also Examples

Description

solar2multic is a utility function to convert the ibd and mibd files (identity by descent) files created by SOLAR into the multic input file mloci.out and convert the phi2 created by SOLAR into the multic input file share.out.

Usage

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solar2multic(phi2, pedigree.file, pedindex.out, pedindex.cde,
             ibd.directory, ibd.dist = NULL, output.directory = ".", 
             delete.fixed.dir = TRUE)

Arguments

phi2

character value specifying a path to a SOLAR-formatted phi2 file. Due to the general size of a typical phi2 file, it is often stored in .gz format. solar2multic will manage this for the user. Whether the user specifies the file with a .gz suffix or not will not effect how solar2multic operates on the file.

pedigree.file

character value specifying a path to a SOLAR-formatted pedigree structure file (.ped). This file must have a header of famid, id, fa, mo, and sex (case insensitive). The file must also be comma separated.

pedindex.out

character value specifying a path to a SOLAR-formatted pedindex.out file. This file must be the same that was output from SOLAR. It provides a mapping between the sequential number system assigned by SOLAR and the original family and individual identifiers.

pedindex.cde

character value specifying a path to a SOLAR-formatted pedindex.cde file. This file must be the same that was output from SOLAR. This file describes how pedindex.out is organized. This is necessary to read pedindex.out correctly.

ibd.directory

character value specifying a path to a directory containing SOLAR-formatted ibd and/or mibd files.

ibd.dist

charater value specifying a path to a SOLAR-formatted .dist file that maps the character marker names to numeric centimorgan values.

output.directory

character value specifying a path to a directory that the output files (mloci.out and share.out) will be placed. If any of the specified directory path does not exist, solar2multic will create the necessary directories.

delete.fixed.dir

logical flag: if TRUE (default), then the temporary directory that is created to hold intermediate files is deleted.

Side Effects

Due to write permissions possibly not allowing the user to gunzip and create files in the specified directory, solar2multic first copies directory and phi2 to the current directory. solar2multic then creates a temporary directory to hold the "fixed," intermediate files that will be deleted (by default). Also, solar2multic will overwrite mloci.out, mloci.out.gz, share.out and share.out.gz if they exist in output.directory.

See Also

solar2mloci, phi2share

Examples

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## Not run: 
solar2multic(phi2 = "phi2.gz",
             pedigree.file = "chrom18.ped",
             pedindex.out = "pedindex.out",
             pedindex.cde = "pedindex.cde",
             ibd.directory = "mibddir",
             output.directory = "multicInput",
             delete.fixed.dir = FALSE)

solar2multic("solarOutput/phi2",
             "solarOutput/chrom10.ped",
             "solarOutput/pedindex.out",
             "solarOutput/pedindex.cde",
             "mibds/chrm10"))

## End(Not run)

multic documentation built on Jan. 15, 2017, 9:30 a.m.