check_maxP {polymapR} | R Documentation |
check your dataset's maxP distribution
Description
Function to assess the distribution of maximum genotype probabilities (maxP
), if these are available. The function
plots a violin graph showing the distribution of the samples' maxP
.
Usage
check_maxP(probgeno_df)
Arguments
probgeno_df |
A data frame as read from the scores file produced by function
saveMarkerModels of R package fitPoly , or alternatively, a data frame containing the following columns:
- SampleName
-
Name of the sample (individual)
- MarkerName
-
Name of the marker
- P0
-
Probabilities of dosage score '0'
- P1...
-
Probabilities of dosage score '1' etc. (up to max dosage, e.g. P4 for tetraploid population)
- maxP
-
Maximum genotype probability identified for a particular individual and marker combination
- maxgeno
-
Most probable dosage for a particular individual and marker combination
- geno
-
Most probable dosage for a particular individual and marker combination, if maxP exceeds a user-defined threshold (e.g. 0.9), otherwise NA
|
Value
This function does not return any value, is simply a visualisation tool to help assess data quality.
Examples
data("gp_df")
check_maxP(gp_df)
[Package
polymapR version 1.1.5
Index]