chao_N0: The Chao estimate of the total number of unseen variants...
In c7rishi/variantprobs: Computing Probabilities of Gene Variants

Description Usage Arguments Details

View source: R/chao_N0.R

The Chao estimate of the total number of unseen variants based on training gene mutation frequencies

1	chao_N0(counts = NULL, r = NULL, N_r = NULL, m)

`counts`	vector of counts or frequencies of the observed variants.
`r`	unique frequencies.
`N_r`	frequency of frequency r.
`m`	training cohort size.

Calculates Chao (1987) estimate of the total number of unseen variants. Also provides an approximate standard error ("se") of the estimate as an attribute, computed using the formula provided in Chao (1987).

## Not run: # load tcga data data("tcga") tcga <- data.table::setDT(tcga) # calculate variant frequencies var_freq <- tcga[, .(v_f = length(unique(patient_id))), by = .(Hugo_Symbol, Variant) ] # calculate cohort size m <- length(unique(tcga$patient_id)) # SGT estimate for t = 0.5, 1, 10 chao_N0(counts = var_freq$v_f, m = m, t = 0.5) ## End(Not run)

c7rishi/variantprobs documentation built on June 23, 2020, 7:42 a.m.