summary.phenotype: Summarize the phenotype data frame

In DavisBrian/seqtools: Sequence Analysis Tools

Description

This function summarizes the phenotype data in a phenotype object.

Usage

## S3 method for class 'phenotype'
summary(p, max.levels = 5L)

summarize_phenotype(p, max.levels = 5L)

Arguments

p	an object of class 'phenotype'.
max.levels	maximum number of levels. See Details

Details

This is an S3 Methdod that calculates basic summary statistics for phenotype data.

For varaibles taking discrete values (logical, integer, charater, and factor) the number of unique values, including NA, are determined. If this is less than or equal to max.levels, then a table of that variable is calcualted. Note: This has no bearing on whether a variable is treated as a categorical varaible in subsequent analysis.

Value

an object of class summary_phenotype.

For numeric variables

• N the number of non-missing data points in the sample.

• Nmiss the number of missing data points in the sample.

• Min the sample minima.

• Max the sameple maxima.

• Median the sample median.

• Mean the sample mean.

• SD the sample standard deviation.

• Q1 the sample first quantile.

• Q3 the sample third quantile.

For (potientially) categorical varaibles

• N the number of non-missing data points in the sample.

• Nmiss the number of missing data points in the sample.

• Levels the number of unique values in the sample.

• Datatype the (R internal) type or storage mode of the sample.

For (potientially) categorical varaibles with Levels <= max.levels a contingency table of counts for each level.

DavisBrian/seqtools documentation built on May 6, 2019, 1:56 p.m.