freq_eval: Calculate the precision, CV, and accuracy of frequency...

In edwardslee/alphabetr: Algorithms for High-Throughput Sequencing of Antigen-Specific T Cells

Description

freq_eval() will evaluated how well freq_estimate performed by calculating the precision and CV of the frequency estimates for the top clones and by determining the proportion of the top clones whose true clonal frequency lies in the 95-percent CI determined by freq_estimate

Usage

freq_eval(freq, number_skewed, TCR, numb_clones, prop_top)

Arguments

freq	The output of freq_estimate
number_skewed	The number of clones represent the top proportion of the T cell population by frequency (this is the same number_skewed argument used when create_clones is called)
TCR	The clonal structure of the simulated T cell population. This is obtained by subsetting the TCR element of the output of create_clones
numb_clones	Total number of distinct clones in the parent population
prop_top	The proportion of the population in frequency represented by the number of clones specified by skewed.

Value

A list with the precision, cv, and accuracy of the frequency estimation.

edwardslee/alphabetr documentation built on May 15, 2019, 11:03 p.m.