Filter markers according with a missing data threshold
filter_missing(
onemap.obj = NULL,
threshold = 0.25,
by = "markers",
verbose = TRUE
)
An 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.
matrix containing HMM emission probabilities
an object of class onemap
.
a numeric from 0 to 1 to define the threshold of missing data allowed
character defining if `markers` or `individuals` should be filtered
A logical, if TRUE it output progress status information.
Cristiane Taniguti, chtaniguti@tamu.edu
data(onemap_example_out)
filt_obj <- filter_missing(onemap_example_out, threshold=0.25)
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