Description Usage Arguments Value Examples
View source: R/exported_functions.R
screen_for_NA_values
identifies and can remove rows or columns of a marker dataset based on the relative frequency of missing values.
1 2 3 |
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? |
A matrix similar to dosage_matrix, with rows or columns removed that had a higher missing value frequency than specified.
1 2 3 4 5 6 7 8 9 | data("segregating_data")
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)
## Not run:
#user input:
#screen_for_NA_values(dosage_matrix=segregating_data, margin=1, cutoff=NULL)
## End(Not run)
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