solar2mloci {multic} | R Documentation |
solar2mloci
reads all of the ibd and mibd files in the given directory,
and creates mloci.out.gz in the specified output directory.
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.
solar2mloci will manage this for the user.
|
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. solar2mloci will manage this
for the user. Whether the user specifies the file with a .gz suffix
or not will not effect how solar2mloci
operates on the file.
|
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,
solar2mloci will overwrite mloci.out and
mloci.out.gz if they exist in
output.directory .
|
delete.fixed.dir |
logical flag: if TRUE , delete the
temporary directory used
to "fix" the SOLAR-formatted ibds and mibd files. This is mostly for
debugging
purposes and is very likely to be not useful to the user community.
|
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
.
## 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)