screen_for_NA_values: Screen marker data for NA values

In polymapR: Linkage Analysis in Outcrossing Polyploids

Screen marker data for NA values

Description

screen_for_NA_values identifies and can remove rows or columns of a marker dataset based on the relative frequency of missing values.

Usage

screen_for_NA_values(
  dosage_matrix,
  margin = 1,
  cutoff = NULL,
  parentnames = c("P1", "P2"),
  plot_breakdown = FALSE,
  log = NULL,
  print.removed = TRUE
)

Arguments

dosage_matrix	An integer matrix with markers in rows and individuals in columns.
margin	An integer at which margin the missing value frequency will be calculated. A value of 1 means rows (markers), 2 means columns (individuals)
cutoff	Missing value frequency cut off. At this frequency, rows or columns are removed from the dataset. If NULL user input will be asked after plotting the missing value frequency histogram.
parentnames	A character vector of length 2, specifying the parent names.
plot_breakdown	Logical. Should the percentage of markers removed as breakdown per markertype be plotted? Can only be used if margin = 1.
log	Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.
print.removed	Logical. Should removed instances be printed?

Value

A matrix similar to dosage_matrix, with rows or columns removed that had a higher missing value frequency than specified.

Examples

data("segregating_data","screened_data")
screened_markers<-screen_for_NA_values(dosage_matrix=segregating_data, margin=1, cutoff=0.1)
screened_indiv<-screen_for_NA_values(dosage_matrix=screened_data, margin=2, cutoff=0.1)

polymapR documentation built on June 22, 2024, 10:34 a.m.