Description Usage Arguments Details Author(s) See Also Examples
Remove columns (genos) that have too many missing values. All genos that have more than perc.snp
values missing in both case.ped
AND control.ped
files will be removed.
1 2 3 | pre2.remove.genos(file.dat, case.ped, control.ped, dir.dat, dir.out,
dir.warning = dir.out, perc.snp = 10, perc.patient = 20, empty = "0/0",
num.nonsnp.col = 5)
|
file.dat |
The name of data file as required for MaCH1. The file should be of the format: M SNP1 M SNP2 - Space separated - No header - Column 1: consists of "M" - Column 2: character SNP names |
case.ped |
The name of pedegree data file that contains CASEs in MaCH input format. |
control.ped |
The name of pedegree data file that contains CONTROLs in MaCH input format. |
dir.dat |
The directory name where |
dir.out |
The directory name to which output files should be saved. |
dir.warning |
The directory name to which warnings about patients with too many missing SNPs should go. Defaults to the same place as |
perc.snp |
The percentage (0-100 percent) of maximum empty values allowed for each geno (column). All genos that have more empty values than this threshold will be removed. |
perc.patient |
The percentage (0-100 percent) of empty values allowed for each patient (row). Names of all patients who end up having more empty values than this threshold will be recorded in the warnings file. |
empty |
The representation of a missing SNP value in the file ("0 0", "0/0", "1/1", "N N", etc). |
num.nonsnp.col |
The number of leading columns in the .ped files that do not contain SNP values. The first columns of the file represent non-SNP values (like patient ID, gender, etc). For MaCH1 input format, the |
Remove columns (genos) that have too many missing values. All genos that have more than perc.snp
values missing in both case.ped
AND control.ped
files will be removed.
All patients that have more than perc.patient
values missing will have their IDs written into "warning.<case.ped>.txt" files. Output will be two clean versions of case.ped
and control.ped
files in dir.out
directory, and optionally the warning files in dir.warning
directory.
The following files will be saved after the program is run:
1 2 3 4 5 6 7 8 9 10 11 12 13 | - <file.dat>.removed.dat - the .dat file containing only the SNPs that were not
removed, will be placed in dir.out directory
- <case.ped>.removed.ped - the CASE .ped file without columns that contain too
many missing values based on the thresholds perc.snp; in dir.out directory
- <control.ped>.removed.ped - the CONTROL .ped file without columns that contain
too many missing values based on the thresholds perc.snp;
in dir.out directory
- warning.<case.ped>.txt - file containing warning messages about patients that
have too many SNPs missing (based on perc.patients) in CASE.ped file,
after the removal of bad SNPs.
- warning.<control.ped>.txt - similar to warning.<case.ped>.txt, only for
CONTROL file.
|
Olia Vesselova
pre1.plink2mach
, pre1.plink2mach.batch
,
pre2.remove.genos.batch
, pre3.call.mach
,
pre3.call.mach.batch
1 | print("See the demo 'gendemo'.")
|
[1] "See the demo 'gendemo'."
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