DENDRO.dist: DENDRO specific genetic divergence evaluation function

In zhouzilu/DENDRO: Dna based EvolutioNary tree preDiction by scRna-seq technOlogy

Description

Calculate the cell-to-cell divergence matrix given variant allele read counts, total allele read counts, estimated mutations and sequencing error rate. This method accounts for transcriptional bursting and sequencing error with a Beta-Binomial framework. This function is linear with number of cells and number of mutations.

Usage

DENDRO.dist(X, N, Z, epi = 0.01, show.progress = TRUE)

Arguments

X	An matrix contains variants allele read counts across cell (column) and loci (row).
N	An matrix contains total allele read counts across cell (column) and loci (row).
Z	An mutation indicator matrix (1 for mutation, 0 for normal) across cell (column) and loci (row).
epi	Sequencing error and rare RNA editing combined rate. Default 0.01 according to Illunima.
show.progress	Whether to show the divergence calculation programs. For large and diverse cell population, this function will take some time and we recommend tracking progress.

Value

'dist' returns an object of class '"dist"'. See https://www.rdocumentation.org/packages/stats/versions/3.5.1/topics/dist for more details

Author(s)

Zilu Zhou

References

https://www.rdocumentation.org/packages/stats/versions/3.5.1/topics/dist

Examples

data("DENDRO_demo")
demo_qc = FilterCellMutation(demo$X,demo$N,demo$Z,demo$Info,demo$label)
dist = DENDRO.dist(demo_qc$X,demo_qc$N,demo_qc$Z,show.progress=FALSE)

zhouzilu/DENDRO documentation built on May 21, 2020, 8 p.m.