groupStat {FindMyFriends} | R Documentation

## Calculate statistics about each gene group

### 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)

[Package FindMyFriends version 1.17.0 Index]