Produce empty object to avoid code break. Function for internal purpose.
empty_onemap_obj(vcf, P1, P2, cross)
An empty object of class onemap
, i.e., a list with the following
components:
a matrix with integers indicating the genotypes read for each marker. Each column contains data for a marker and each row represents an individual.
number of individuals.
number of markers.
a vector with the
segregation type of each marker, as strings
.
a
vector with the segregation type of each marker, represented in a
simplified manner as integers, i.e. 1 corresponds to markers of type
"A"
; 2 corresponds to markers of type "B1.5"
; 3 corresponds
to markers of type "B2.6"
; 4 corresponds to markers of type
"B3.7"
; 5 corresponds to markers of type "C.8"
; 6 corresponds
to markers of type "D1"
and 7 corresponds to markers of type
"D2"
. Markers for F2 intercrosses are coded as 1; all other crosses
are left as NA
.
the name of the input file.
number of phenotypes.
a matrix with phenotypic values. Each column contains data for a trait and each row represents an individual.
object of class vcfR
character with parent 1 ID
character with parent 2 ID
type of cross. Must be one of: "outcross"
for full-sibs;
"f2 intercross"
for an F2 intercross progeny; "f2 backcross"
;
"ri self"
for recombinant inbred lines by self-mating; or
"ri sib"
for recombinant inbred lines by sib-mating.
Cristiane Taniguti, chtaniguti@tamu.edu