reorder_scaffolds: Reorder scaffolds based on assignment to chromosomes.

In nwvankuren/genomics-plotting: Utilities for plotting statistics from genome-wide analyses

Description

This function will reorder the results of a genome-wide statistical analysis based on the contents of a file that assigns each scaffold to a reference genome assembly. The assignments can be generated using, e.g. OrderScaffoldsByBlatingProteins.pl, but must have the following columns:

scaf, scafLen, chr, strand, median_pos

where scaf is scaffold name, scafLen is the scaffold length, chr is the chromosome assignment, strand is the direction of the scaffold relative to the chromosome, and median pos is the position of the scaffold along the chromosome. This last bit is used to relatively order the scaffolds and must be increasing along the chromosome length.

The main difficulty is handling the variety of different species' chromosome level assemblies. Some, like Melitaea cinxia and Papilio xuthus follow the convention of "chr1", etc. Others, however, like the Heliconius genomes, haven't specified complete chromosomes and have a unique naming system, typically e.g. Hmel201003o. These need to be handled differently. I can only guarantee that reordering information from the following genomes can currently be handled:

Heliconius melpomene v2.5 (hmel)
H. erato demophoon v1.0 (herd)
Bombyx mori chromosome (bmor)
Papilio xuthus chromosome (pxut)
Melitaea cinxia (mcin)

The appropriate abbreviation should be supplied to the "species" argument to the reordering function.

Usage

reorder_scaffolds(input, assignments, species)

Arguments

input	A tibble containing scaffold, ps, stat, and chr as the first three columns.
assignments	Name of the file containing the reordering information.
species	The abbreviation for the species assembly you ordered to.

Value

Returns the input tibble with chr colun detailing which reference genome chromosomes the draft genome scaffolds map to. Only input rows that reside on mapped scaffolds are included.

Examples

a1 <- system.file("extdata", "test.gemma_gwas.txt.gz",
                  package = "gwplotting")

a2 <- system.file("extdata", "test.reordering.txt.gz",
                  package = "gwplotting")

b <- load_gemma_gwas( a1, pval = 'p_wald' )
b <- reorder_scaffolds( input = b, assignments = a2, species = 'pxut' )
b

nwvankuren/genomics-plotting documentation built on April 14, 2021, 1:18 a.m.