multic (version 0.3.2)

sw2mloci: Convert SimWalk IBD files into a single mloci.out.

Description

sw2mloci converts all IBD files in a given directory into a sinlge mloci.out needed my multic, altering the centimorgan values if a map argument is provided.

Usage

sw2mloci(ibd.directory, map="", output.directory=".", famid = NULL, id = NULL, dadid = NULL, momid = NULL, directory = NULL)

Arguments

ibd.directory

a character object specifying the name of the directory that contains the SimWalk IBD files. This can be an absolute or relative path.

map

a character object specifying the name of a .map file to be used to modify the centimorgan values in the mloci.out file. This can be an absolute or relative path and does not have to be in the same directory as the parameter ibd.directory.

output.directory

a character object specifying the name of the directory to put the finished mloci.out.gz. This can be an absolute or relative path. If the directory does not exist, it will be created.

famid

Vector of family id values.

id

Vector of individual id values.

dadid

Vector of father id values.

momid

Vector of mother id values

directory

Deprecated -- replaced by ibd.directory, but included for backward compatibility. If not NULL and ibd.directory is NULL, then its value is assigned to ibd.directory.

Value

• a character object specifying the name of the file created. In general, this will be "mloci.out.gz".

Side Effects

If a file named "mloci.out" or "mloci.out.gz" already exist in the current directory, sw2mloci will move them to "mloci.out.before" or "mloci.out.before.gz" respectively before doing any calculations. sw2mloci also copies the IBD files and map file (if it is specified) to a temp space. This is done to bypass any write permission issues. This temp space is deleted when the function is finished. It also creates a temp space to hold the intermediate mibd files. These also will be deleted at the end of the function.

See Also

There are similar functions to deal with SOLAR mibds, see phi2share, solar2mloci, and solar2multic.

Examples

sw2mloci("../otherInput/sw18", "../otherInput/sw18/c18.map")

sw2mloci("sw18")

sw2mloci(".", "sw18/c18.map", output.directory = "multicInput")