read_fitpoly {mappoly}

Data Input in fitPoly format

Description

Reads an external data file generated as output of saveMarkerModels. This function creates an object of class mappoly.data.

Usage

read_fitpoly(
  file.in,
  ploidy,
  parent1,
  parent2,
  offspring = NULL,
  filter.non.conforming = TRUE,
  elim.redundant = TRUE,
  parent.geno = c("joint", "max"),
  thresh.parent.geno = 0.95,
  prob.thres = 0.95,
  file.type = c("table", "csv"),
  verbose = TRUE
)

Arguments

file.in

a character string with the name of (or full path to) the input file

ploidy

the ploidy level

parent1

a character string containing the name (or pattern of genotype IDs) of parent 1

parent2

a character string containing the name (or pattern of genotype IDs) of parent 2

offspring

a character string containing the name (or pattern of genotype IDs) of the offspring individuals. If NULL (default) it considers all individuals as offsprings, except parent1 and parent2.

filter.non.conforming

if TRUE (default) converts data points with unexpected genotypes (i.e. no double reduction) to 'NA'. See function segreg_poly for information on expected classes and their respective frequencies.

elim.redundant

logical. If TRUE (default), removes redundant markers during map construction, keeping them annotated to in order to include them in the final map.

parent.geno

indicates whether to use the joint probability 'joint' (default) or the maximum probability of multiple replicates (if available) to assign dosage to parents. If there is one observation per parent, both options will yield the same results.

thresh.parent.geno

threshold probability to assign a dosage to parents. If the probability is smaller than thresh.parent.geno, the marker is discarded.

prob.thres

threshold probability to assign a dosage to offspring. If the probability is smaller than prob.thres, the data point is converted to 'NA'.

file.type

indicates whether the characters in the input file are separated by 'white spaces' ("table") or by commas ("csv").

verbose

if TRUE (default), the current progress is shown; if FALSE, no output is produced

Value

An object of class mappoly.data which contains a list with the following components:

ploidy

ploidy level

n.ind

number individuals

n.mrk

total number of markers

ind.names

the names of the individuals

mrk.names

the names of the markers

dosage.p1

a vector containing the dosage in parent P for all n.mrk markers

dosage.p2

a vector containing the dosage in parent Q for all n.mrk markers

chrom

a vector indicating which sequence each marker belongs. Zero indicates that the marker was not assigned to any sequence

genome.pos

Physical position of the markers into the sequence

seq.ref

NULL (unused in this type of data)

seq.alt

NULL (unused in this type of data)

all.mrk.depth

NULL (unused in this type of data)

geno.dose

a matrix containing the dosage for each markers (rows) for each individual (columns). Missing data are represented by ploidy_level + 1

n.phen

number of phenotypic traits

phen

a matrix containing the phenotypic data. The rows correspond to the traits and the columns correspond to the individuals

kept

if elim.redundant = TRUE, holds all non-redundant markers

elim.correspondence

if elim.redundant = TRUE, holds all non-redundant markers and its equivalence to the redundant ones

Author(s)

Marcelo Mollinari, [e-mail]

References

Voorrips, R.E., Gort, G. & Vosman, B. (2011) Genotype calling in tetraploid species from bi-allelic marker data using mixture models. _BMC Bioinformatics_. doi:10.1186/1471-2105-12-172

Examples

#### Tetraploid Example
ft <- "https://raw.githubusercontent.com/mmollina/MAPpoly_vignettes/master/data/fitpoly.dat"
tempfl <- tempfile()
download.file(ft, destfile = tempfl)
fitpoly.dat <- read_fitpoly(file.in = tempfl, ploidy = 4, 
                            parent1 = "P1", parent2 = "P2", 
                            verbose = TRUE)
print(fitpoly.dat, detailed = TRUE)
plot(fitpoly.dat)
plot_mrk_info(fitpoly.dat, 37)