project.missfilter: project.missfilter
In mtmcgowan/GGcall: Clusters Infinium SNP chip data in polyploid species and calls genotypes
Description
Usage
Arguments
Value
View source: R/project.missfilter.R
Description
Checks for problematic samples and markers. Samples with a set missing rate are flagged. Markers with zero-variance (either all theta or R values are the same) are also flagged for removal.
Usage
1
project.missfilter(project, missrate = 0.2, type = "raw")
Arguments
project
a project object from imported GenomeStudio data
missrate
The missing rate threshold where markers with a proportion of NA values above this threshold will be removed (default = 0.2 i.e. 20% cutoff)
type
Which type of data should be check. GenomeStudio theta/R values will have more missing values than the raw X/Y. (either 'raw' or 'GSnorm')
Value
A project object with filter flags applied to markers
mtmcgowan/GGcall documentation built on July 1, 2021, 4:14 a.m.
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Description Usage Arguments Value
View source: R/project.missfilter.R
Description
Checks for problematic samples and markers. Samples with a set missing rate are flagged. Markers with zero-variance (either all theta or R values are the same) are also flagged for removal.
Usage
1 | project.missfilter(project, missrate = 0.2, type = "raw")
|
Arguments
project |
a project object from imported GenomeStudio data |
missrate |
The missing rate threshold where markers with a proportion of NA values above this threshold will be removed (default = 0.2 i.e. 20% cutoff) |
type |
Which type of data should be check. GenomeStudio theta/R values will have more missing values than the raw X/Y. (either 'raw' or 'GSnorm') |
Value
A project object with filter flags applied to markers
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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