score.variant.status: Take the dataframe with variants and status and determine...
In KinformR: Relationship-Informed Pedigree and Variant Scoring
score.variant.status R Documentation
Take the dataframe with variants and status and determine which indivudals
are scored correctly and which are scored incorrectly.
Assign an A.c, A.i, U.c, U.i, unk
Description
Variants can be encoded as binary (0 or 1, genotypes 0/0 or 0/1, or phased genotypes 0|0 0|1).
Note the program assumes alt is the disease allele. homozygous alts are allowed.
Usage
score.variant.status(indiv.df, theoretical.max = FALSE)
Arguments
indiv.df
A dataframe with the format:
name status variant
MS-5678-1001 A 0/1
theoretical.max
Should the theoretical maxima be returned instead of the observed values?
When true, the scoring assumes correct variant-status pair for each individual.
Default is FALSE.
Details
theoretical.max - bool, default is FALSE
when TRUE, function encodes the theoretical max,
using a dummy perfect associatng variant generated to see what a family could score.
TODO - switch to numbers 1-4 and -1?
Value
Copy of input dataframe, with dataframe with the status categroies added as a new column "statvar.cat"
KinformR documentation built on Feb. 17, 2026, 5:07 p.m.
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| score.variant.status | R Documentation |
Take the dataframe with variants and status and determine which indivudals are scored correctly and which are scored incorrectly. Assign an A.c, A.i, U.c, U.i, unk
Description
Variants can be encoded as binary (0 or 1, genotypes 0/0 or 0/1, or phased genotypes 0|0 0|1). Note the program assumes alt is the disease allele. homozygous alts are allowed.
Usage
score.variant.status(indiv.df, theoretical.max = FALSE)
Arguments
indiv.df |
A dataframe with the format: name status variant MS-5678-1001 A 0/1 |
theoretical.max |
Should the theoretical maxima be returned instead of the observed values? When true, the scoring assumes correct variant-status pair for each individual. Default is FALSE. |
Details
theoretical.max - bool, default is FALSE when TRUE, function encodes the theoretical max, using a dummy perfect associatng variant generated to see what a family could score. TODO - switch to numbers 1-4 and -1?
Value
Copy of input dataframe, with dataframe with the status categroies added as a new column "statvar.cat"
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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