groupStat: Calculate statistics about each gene group

In FindMyFriends: Microbial Comparative Genomics in R

Description

This method calculates a range of statistics and positional information about each gene group. The information returned are. Maximum number of genes from the same organism (paralogues), shortest sequence length, longest sequence length, standard deviation of sequence lengths, index of genes in group, downstream and upstream gene groups.

Usage

groupStat(object, ...)

## S4 method for signature 'pgVirtual'
groupStat(object, vicinity = 1)

Arguments

object	A pgVirtual subclass
...	parameters passed on.
vicinity	An integer given the number of flanking gene groups to traverse

Value

A list with an element for each gene group, each with the following elements.

maxOrg

The highest number of distinct genes from the same organism present in the group. A number above 1 indicate the presence of paralogues.

minLength

The length of the shortest sequence in the group.

maxLength

The length of the longest sequence in the group.

sdLength

The standard deviation of lengths in the group.

genes

The index for the genes present in the group.

backward

A character vector with gene groups separated by ';' that lies downstream of the gene group. The number of gene groups for each gene is controlled by the flankSize argument. If the contig stops before the required number of flanking genes have been reached, NA will be added. Downstream is defined in relation to the strand of the contig/chromosome, and not the translational direction of the gene in question.

forward

As above in the other direction.

Methods (by class)

• pgVirtual: Group statistics for all pgVirtual subclasses

Examples

testPG <- .loadPgExample(withGroups=TRUE)

grStats <- groupStat(testPG)

FindMyFriends documentation built on Nov. 8, 2020, 6:46 p.m.