phi2share {multic} | R Documentation |
phi2share
reads in the specified files
and generates a multic-formatted share.out file. share.out contains
unique identifiers, expected shared genetic material, and sibling,
spousal, and parent-offspring true/false values.
phi2share(phi2, pedigree.file, pedindex.out, pedindex.cde, output.directory=".")
phi2 |
a character value to specify the location of a SOLAR-formatted phi2
(or similarly formatted) file. Due to the general size of a typical
phi2 file, it is
often stored in .gz format. phi2share
will manage this for the user.
Whether the user specifies the file with a .gz suffix or not will not
effect how phi2share operates on the
file.
|
pedigree.file |
a character value to specify the location of a .ped (or
similarly formatted) file. This file must have a header of
famid , id ,
fa , mo ,
and sex (case insensitive). The file
must also be comma separated.
|
pedindex.out |
a character value to specify the location of a 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 |
a character value to specify the location of a 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. |
output.directory |
a character value specifying which directory to place the output
share.out. If output.directory
(including supporting path) does not exist yet,
it will be created. The default directory is the current directory.
|
phi2share
creates a local copy of,
gunzip's, and removes the copy of phi2
.
It also will overwrite share.out and share.out.gz
if they exist in output.directory
.
## Not run: phi2share(phi2 = "phi2", pedigree.file = "chrom18.ped", pedindex.out = "pedindex.out", pedindex.cde = "pedindex.cde", output.directory = "multicInput") phi2share("solarOutput/phi2.gz", "solarOutput/chrom18.ped", "solarOutput/pedindex.out", "solarOutput/pedindex.cde") ## End(Not run)