Description Usage Arguments Side Effects See Also Examples
solar2mloci
reads all of the ibd and mibd files in the given directory,
and creates mloci.out.gz in the specified output directory.
1 2 3 | solar2mloci(directory, phi2, pedindex.out, pedindex.cde,
ibd.dist = NULL, output.directory = ".",
delete.fixed.dir = TRUE)
|
directory |
charater value specifying a path to a directory of SOLAR-formatted
ibd and/or mibd files. These files are often kept in .gz format.
|
phi2 |
charater 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. |
pedindex.out |
character value specifying a path to a SOLAR-formatted pedindex.out file. This must be the same file 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 must be the same file that was output from SOLAR. This file describes the format of pedindex.out. This is necessary to read pedindex.out correctly. |
ibd.dist |
charater value specifying a path to a SOLAR-formatted .dist file that maps the character marker names of ibd files to their corresponding numeric centimorgan values. |
output.directory |
charater value specifying a path to a directory where the output file
mloci.out.gz will be created. If the directory (including supporting
path) does not exist yet, it will be created. Also,
|
delete.fixed.dir |
logical flag: if |
Due to write permissions possibly not allowing the user to gunzip
and create files in the specified
directory
,
solar2mloci
first copies
directory
and
phi2
to the current directory.
solar2mloci
then
creates a temporary directory to hold the "fixed," intermediate files
that will be deleted (by default). Also,
solar2mloci
will overwrite
mloci.out and mloci.out.gz if they exist in
output.directory
.
1 2 3 4 5 6 7 8 9 10 | ## Not run:
solar2mloci(directory = "ibddir", phi2 = "phi2",
pedindex.out = "pedindex.out", pedindex.cde = "pedindex.cde",
ibd.dist = "solar.dist", output.directory = "multicInput",
delete.fixed.dir = FALSE)
solar2mloci("mibds/chrm10", "solarOutput/phi2.gz",
"solarOutput/pedindex.out", "solarOutput/pedindex.cde")
## End(Not run)
|
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