groupStat: 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, ...)
"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