checkped: Check a pedigree
In luansheng/visPedigree: Tidying and visualization for animal pedigree
checkped R Documentation
Check a pedigree
Description
checkped function checks a pedigree.
Usage
checkped(ped, addgen = TRUE)
Arguments
ped
A data.table or data frame including the pedigree, which including the first three columns: individual, sire and dam IDs. More columns, such as sex, generation can be included in the pedigree file. Names of the three columns can be assigend as you would like, but their orders must be not changded in the pedigree. Individual ID should not be coded as "", " ", "0", asterisk, and "NA", otherwise these individuals will be deleted from the pedigree. Missing parents should be denoted by either "NA", "0", asterisk. Space and "" will also be recoded as missing parents, but not be recommended.
addgen
A logical value indicates whether individual generation number will be generated. The default values is TRUE, then a new column named Gen will be added in the returned data.table.
Details
This function takes a pedigree, detects missaing parents, checks duplicated, bisexual individuals, adds missing founders, and sorts the pedigree. All individuals's sex will be inferred if there is not sexual information in the pedigee. If the pedigree includes the column Sex, then individuals's sexes need to be recoded as "male", "female", or NA (unknown sex). Missing sexes will be identified from the pedigree structure and be added if possible.
Value
A data.table including the checked pedigree is returned. Individual, sire and dam ID columns are renamed as Ind, Sire and Dam. Missing parent is replacted with the default missing value NA. The column Sex includes individuals' sex (male or female, NA for unknown sex). The column Gen will be included when the parameter addgen is TRUE. Ind, Sire, Dam and Sex columns are character; The Gen column is integer.
luansheng/visPedigree documentation built on Feb. 4, 2023, 11:10 p.m.
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.
| checkped | R Documentation |
Check a pedigree
Description
checkped function checks a pedigree.
Usage
checkped(ped, addgen = TRUE)
Arguments
ped |
A data.table or data frame including the pedigree, which including the first three columns: individual, sire and dam IDs. More columns, such as sex, generation can be included in the pedigree file. Names of the three columns can be assigend as you would like, but their orders must be not changded in the pedigree. Individual ID should not be coded as "", " ", "0", asterisk, and "NA", otherwise these individuals will be deleted from the pedigree. Missing parents should be denoted by either "NA", "0", asterisk. Space and "" will also be recoded as missing parents, but not be recommended. |
addgen |
A logical value indicates whether individual generation number will be generated. The default values is TRUE, then a new column named Gen will be added in the returned data.table. |
Details
This function takes a pedigree, detects missaing parents, checks duplicated, bisexual individuals, adds missing founders, and sorts the pedigree. All individuals's sex will be inferred if there is not sexual information in the pedigee. If the pedigree includes the column Sex, then individuals's sexes need to be recoded as "male", "female", or NA (unknown sex). Missing sexes will be identified from the pedigree structure and be added if possible.
Value
A data.table including the checked pedigree is returned. Individual, sire and dam ID columns are renamed as Ind, Sire and Dam. Missing parent is replacted with the default missing value NA. The column Sex includes individuals' sex (male or female, NA for unknown sex). The column Gen will be included when the parameter addgen is TRUE. Ind, Sire, Dam and Sex columns are character; The Gen column is integer.
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.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.