solar2multic {multic} | R Documentation |
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.
solar2multic(phi2, pedigree.file, pedindex.out, pedindex.cde, ibd.directory, ibd.dist = NULL, output.directory = ".", delete.fixed.dir = TRUE)
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.
|
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
.
## 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)