create_segsites | R Documentation |
These functions create and modify segregating sites objects, which are one of the basic intermediary statistics that is calculated in coala. Segregating sites consist primarily of a SNP matrix that contains all SNPs for one locus, with some additional information attached. The parts of the S3 class are detailed below.
create_segsites(snps, positions, trio_locus = numeric(0), check = TRUE)
get_snps(segsites)
get_positions(segsites)
set_positions(segsites, positions)
get_trio_locus(segsites)
set_trio_locus(segsites, trio_locus)
is_segsites(segsites)
create_locus_trio(left, middle, right)
snps |
The SNP Matrix (see Details). |
positions |
A numeric vector indicating the relative positions of each SNP on the locus (see Details). |
trio_locus |
If the locus consists of a locus trio (see Details). |
check |
Whether non-segregating sites are removed from the segregating
sites ( |
segsites |
The segregating sites object |
left |
The segregating sites from the left locus |
middle |
The segregating sites from the middle locus |
right |
The segregating sites from the right locus |
A segregating sites object contains all SNPs for one genetic locus. Each object consists of three parts: A SNP matrix, a vector of SNP positions and a vector that states which transcript a SNP belong to, if the locus consists of multiple transscripts ('locus trio').
In the SNP matrix, each row represents a haplotype and each
column represents a SNP. An entry is either 1
if the
haplotype carries the derived allele for the SNP, or 0
if it
carries the ancestral one.
In the positions vector, each entry gives the relative position of SNP in the corresponding column of the SNP matrix.
The trio_locus vector contains the trio locus each SNP
belongs to. Entry of -1
,0
, 1
represent the
left, middle, and right locus, respectively. For normal loci,
this just consists of 0
's
create_segsites()
: Creates segregating sites
get_snps()
: Returns the SNP matrix from a segregating sites
object.
get_positions()
: Returns the SNP's positions from a segregating
sites object.
set_positions()
: Sets the SNP's positions in a segregating
sites object.
get_trio_locus()
: Returns the trio locus positions from a
segregating sites object.
set_trio_locus()
: Sets the trio locus in a segregating sites
object.
is_segsites()
: Checks whether an object is a segsites object.
create_locus_trio()
: Combines three segregating sites to a locus trio
Paul Staab
For converting biological data to segsites: as.segsites
snps <- matrix(c(1, 0, 0,
1, 1, 0,
0, 0, 1), 3, 3, TRUE)
pos <- c(.1, .3, .5)
segsites <- create_segsites(snps, pos)
print(segsites)
get_snps(segsites)
get_positions(segsites)
# When subsetting individuals, sites that are not
# segregating in these are automatically removed:
segsites[1:2, 1:3]
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