dXX_index: dXX_index

In Benjamin-Vincent-Lab/binfotron: Binfotron Bioinformatics Analysis Tools Suite

dXX_index

Description

From vdjtools: "The estimate equals to 1 - n / N, where n is the minimum number of clonotypes accounting for at least XX of clonotypes in the sample. Computes diversity index that equals to one minus the minimum fraction of clonotypes accounting for at least 50 reads."

Usage

dXX_index(my_counts, my_fraction, should_screen_counts = TRUE)

Arguments

my_counts	vector of postive integers
should_screen_counts	Boolean to indicate if the coutns should be screened for valid data. Set to false if the data has already been checked by another function.

Value

Typically called d50_index. Computes the diversity index dXX, where XX is a specified fraction.

See Also

Other diversity: chao1(), evenness(), get_corrected_entropy_rdata_2_4096_path(), get_corrected_entropy_rdata_4097_65536_path(), get_corrected_entropy_rdata_ab1025_65K_ent1_8_path(), get_corrected_entropy_rdata_ab8_1024_ent1_8_path(), has_sufficient_abundance_for_entropy(), inv_simpson(), predict_true_entropy_from_counts(), predict_true_entropy_from_diversity(), screen_counts(), shannon_entropy()

Benjamin-Vincent-Lab/binfotron documentation built on Oct. 1, 2024, 8:33 p.m.