R/prep_gsp_for_hap_dropping.R
prep_gsp_for_hap_dropping.RdJust a simple function that makes a list-based data structure that makes it easy to gene-drop chromosome segments down the gsp. The basic idea is to get everyone into a data structure in which they are ordered such that by the time you get to segregating segments from anyone, you already have the segments segregated into them. This works by each individual having a list of gametes (post-recombination) coming out of them, and a list of "uniters" which are the gametes coming into them. We just point the uniters to gametes in the previous generation and then make sure that we shuffle the order of the gametes when they come out of someone.
prep_gsp_for_hap_dropping(gsp)A tibble that holds the genome simulation pedigree (GSP). This is a tibble in which each row specifies an individual in the GSP. The columns of the tibble are:
ind: a numeric identifier for that row's indvidual.
par: the numeric ID of the first parent of the individual (NA if the
individual is a founder of the pedigree).
par2: the numeric ID of the second parent of the individual (NA if
the individual is a founder)
ipar1: the number of gametes that par1 must segregate "through" ind in
order to exhaust all the genetic material in the GSP. These values are given
by the red numerals alongside the edge connecting parents to offspring in the
GSP images defined by gsp2dot(). See the vignette gscramble-tutorial, for
an example. (NA if ind is a founder).
ipar2: the number of gametes that par2 must segregate through ind.
(NA if ind is a founder).
hap1: a unique character label given to the first haplotype in ind if ind is a
founder. If ind is not a founder, this must be NA.
hap2: unique character label given to the second haplotype in ind. NA if ind
is not a founder.
hpop1: character label giving the population of origin of the first haplotype
(i.e., hap1) in ind, if ind is a founder. NA otherwise.
hpop2: character label giving the population of origin of the second
haplotype (i.e., hap2) in ind. NA if ind is not a founder.
sample: unique character label for the outcoming diploid sample from the
pedigree member ind. NA if ind is not sampled.
osample: the number of diploid samples that come out of ind. NA if
ind is not sampled.
This function returns a named list, which is a linked-list type of
structure that contains the same information that is in gsp, but
it makes it easier to access when traversing the pedigree.
The length of the list is
nrow(gsp). The names are the character versions of the ind column.
Each component of the list refers to an individual row from gsp. All
of these list elements are themselves lists. (i.e., the information
about a single individual is stored in a list.) Every such individual
list has at least the two elements:
isSample: TRUE if samples are taken from the individual. FALSE otherwise.
isFounder: TRUE if the individual is a founder. FALSE otherwise.
nGamete: The total number of gametes that will be segregated out
of this individual along edges to the offspring of the individual in the pedigree.
This is the sum of all the red numbers alongside edges below the individual in the
GSP.
If an individual's isSample is TRUE, then its list also contains the following elements:
nSamples: the number of diploid genomes sampled out of this individual.
This is the purple number along the edge to the sample node below the individual
in the GSP "picture".
If an individual's, isFounder is TRUE then its list also contains
the following elements:
hpop1: the population from which haplotype 1 in this (founder) individual originated.
hpop2: the population from which haplotype 2 in this (founder) individual originated.
fh_idx1: this stands for "founding haplotype index 1. It is a unique integer
that identifies haplotype one in this founder individual. This integer is unique over
all haplotypes in all the founder individuals.
fh_idx2' the unique integer identifier for haplotype two in this founder
individual.
If an individual's isFounder is FALSE, then its list also contains
the following elements:
par1 and par2. Each of these is a list with the elements:
par: the character identifier of the first (if in par1) of the
second (if in par2) parent of the individual.
gam_idx: This tells us which of the gametes in the parent (1 or 2)
depending on if this is in par1 or par2, gets segregated to the
individual. NEED TO EXPLAIN MORE. SINCE THINGS GET PERMUTED, ETC.
# get the 13 member complex pedigree in tibble form as the
# package data object GSP and prep it:
GSP_list <- prep_gsp_for_hap_dropping(GSP)