QCGWAS (version 1.0-9)

convert_impstatus: Convert imputation-status values to the QCGWAS standard

Description

Converts imputation-status data to the standard values used by QC_GWAS

Usage

convert_impstatus(impstatus,
                  T_strings = c("1", "TRUE", "T"),
                  F_strings = c("0", "FALSE", "F"),
                  NA_strings = c(NA, "NA", ".", "-"),
                  use_log = FALSE, ...)

Arguments

impstatus

vector of imputation-status data.

T_strings

character-string(s) indicating imputed data.

F_strings

character-string(s) indicating genotyped data.

NA_strings

character-string(s) indicating missing data.

use_log, …

arguments used by QC_GWAS; redundant when convert_impstatus is used separately.

Value

Numeric vector with values 0 for genotyped, 1 for imputed and NA for unknown data.

Details

This function is used to convert the imputation-status column into the standard format, where 0 is genotyped and 1 is imputed. Untranslated values (i.e. strings that do not appear in any of the string arguments) will trigger a warning message and are set to NA.

Examples

# NOT RUN {
  status1 <- c(0,0,0,1,1,1,2,NA)
  status2 <- c(TRUE, FALSE, TRUE, FALSE, NA)
  status3 <- c("imputed", "genotyped", "NA", NA)
  status4 <- c(status1, status2, status3)
  
  ( outcome1 <- convert_impstatus(status1,
                                  T_strings = 1,
                                  F_strings = 0,
                                  NA_strings = NA) )
  # status 1 contains an untranslated value "2", which is
  # converted to NA. To avoid the warning message:
  
  ( outcome1 <- convert_impstatus(status1,
                                  T_strings = 1,
                                  F_strings = 0,
                                  NA_strings = c(NA, 2)) )
  
  
  ( outcome2 <- convert_impstatus(status2,
                                  T_strings = TRUE,
                                  F_strings = FALSE,
                                  NA_strings = NA) )
  
  ( outcome3 <- convert_impstatus(status3,
                                  T_strings = "imputed",
                                  F_strings = "genotyped",
                                  NA_strings = c("NA", NA)) )
  # Note that NA_strings includes both the character-string "NA"
  # and the value NA. Otherwise, one of the two would go 
  # "untranslated" and trigger a warning message.
  
  
  # And to check them all together
  ( outcome4 <- convert_impstatus(status4,
                          T_strings = c(1, TRUE, "imputed"),
                          F_strings = c(0, FALSE, "genotyped"),
                          NA_strings = c("NA", NA, 2)) )
# }