View source: R/submapSummary.r
submapSummary | R Documentation |
This function creates a summary on the submaps created.
submapSummary(submaps, a.threshold = 1)
submaps |
a list of submaps |
a.threshold |
the maximum value for a (default is 1) |
This function gives for each genotyped individual summary statistics about the calculations.
This function returns a dataframe with 13 columns :
- famid : family identifier
- id : individual identifier
- pheno : phenotype (1 non affected, 2 affected, 0 unknown)
- submaps : number of valid submaps (i.e. submaps with a < a.threshold)
- quality: percentage of valid submaps
- f_min: minimum f on valid submaps
- f_max: maximum f on valid submaps
- f_mean: mean f on valid submaps
- f_median: median f on valid submaps (recommended to estimate f)
- a_median: median a on valid submaps (recommended to estimate a)
- pLRT_median: median p-value of LRT tests on valid submaps
- inbred: a flag indicating if the individual is inbred (pLRT_median <0.05) or not
- pLRT_<0.05: number of valid submaps with a LRT having a p-value below 0.05
this function returns a dataframe.
setSummary
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