Description Usage Arguments Value Examples
View source: R/cumulative_frequency.R
obtain cumulative allele frequency of rare lof and functional variants
1 | get_cumulative_frequencies(vars, threshold = 0.01)
|
vars |
dataframe of variants (one row per allele), which includes the number of times that allele was observed within the population, as well as the total number of alleles in the population. Alternatively, this can be a list of dataframe, each for a different population |
threshold |
minor allele frequency (MAF) threshold, we exclude variants with MAF values above or equal to this threshold. This needs to be matched to the thresh9old used during identification of the biallelically inherited genotypes. |
a list of loss of function cumulative frequency, functional cumulative frequency and synonymous cumulative frequency. Alternatively, if the function was prvoided with a list of dataframe, return a list of frequency lists, named as per the input list.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | vars = read.table(header = TRUE, text = "
CHROM POS REF ALT AC AN CQ
1 1 A G 1 1000 missense_variant
1 2 G C 1 1000 stop_gained
1 3 T A 1 1000 stop_lost
1 4 G T 1 1000 synonymous_variant")
get_cumulative_frequencies(vars)
vars2 = read.table(header = TRUE, text = "
CHROM POS REF ALT AC AN CQ
1 1 A G 1 1000 missense_variant
1 2 G C 1 1000 stop_gained
1 3 T A 1 1000 stop_lost
1 4 G T 1 1000 synonymous_variant")
var_list = list("first"=vars, "second"=vars2)
get_cumulative_frequencies(var_list)
threshold = 0.005
get_cumulative_frequencies(var_list, threshold)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.