filter_missing function

Filter markers according with a missing data threshold

filter_missing(
  onemap.obj = NULL,
  threshold = 0.25,
  by = "markers",
  verbose = TRUE
)

Arguments

• onemap.obj: an object of class onemap.
• threshold: a numeric from 0 to 1 to define the threshold of missing data allowed
• by: character defining if markers or individuals should be filtered
• verbose: A logical, if TRUE it output progress status information.

Returns

An object of class onemap, i.e., a list with the following components: - geno: a matrix with integers indicating the genotypes read for each marker. Each column contains data for a marker and each row represents an individual. - n.ind: number of individuals.

• n.mar: number of markers. - segr.type: a vector with the segregation type of each marker, as strings. - segr.type.num: 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. - input: the name of the input file.

• n.phe: number of phenotypes. - pheno: a matrix with phenotypic values. Each column contains data for a trait and each row represents an individual. - error: matrix containing HMM emission probabilities

Examples

data(onemap_example_out)
  filt_obj <- filter_missing(onemap_example_out, threshold=0.25)

Author(s)

Cristiane Taniguti, chtaniguti@tamu.edu