summariseDist: Attach new columns summarising distance measurements to LMM...

In wanyuac/GeneMates: Analysing association and physical linkage between bacterial genes

Attach new columns summarising distance measurements to LMM results (lmms)

Description

This function produces summary statistics of distance measurements per pair of alleles.

Usage

summariseDist(
  lmms,
  lmms.ds,
  tree,
  clades,
  allele.pam,
  max.nodes = -1,
  max.dist = Inf,
  colname.pair = "pair",
  colname.co = "n_xy",
  qs = c(0, 0.25, 0.5, 0.75, 1),
  n.cores = n.cores
)

Arguments

lmms	a data frame that must contain two columns x and y for allele names.
lmms.ds	a data frame sharing the columns x and y of lmms and all of their distance measurements.
tree	A phylogenetic tree (an object of the phylo class defined in the ape package) accompanying the clades argument.
clades	A PAM of samples in every clade. It can be obtained using the function tree2Clade.
allele.pam	an allelic PAM of bacterial genes. Usually it is the element A in the output list of the function importAllelicPAM.
max.nodes	an integer specifying the maximal number of nodes to which we can trust paths for distance measurements. Set max.nodes = -1 to skip this fiter when the accuracy of measurements does not matter. Notice node number equals zero for overlapping genes.
max.dist	An inclusive upper bound for filterring distance measurements. Measurements above this threshold will be ignored. Set it to Inf to turn off this filter.
colname.pair	a column name in the data frame lmms for indices of a pair of alleles
colname.co	a column name in the data frame lmms for the number of co-occurrence
qs	quantile probabilities (between 0 and 1, inclusive) of physical distances. The minimum, first quantile (25th percentile), median, third quantile (75th percentile) and the maximum will always be calculated.
n.cores	Number of computational cores that will be used in parallel for this function.

Author(s)

Yu Wan ([e-mail])

wanyuac/GeneMates documentation built on Aug. 12, 2022, 7:37 a.m.