convert_impstatus {QCGWAS} | R Documentation |
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 |
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
.
Value
Numeric vector with values 0
for genotyped, 1
for imputed and NA
for unknown data.
Note
The implementation of this function has changed. Previously, only character data was translated using the string arguments. Since version 1.0-4, the string arguments are used for all data types, so the user can determine the conversion of logical and numeric values as well.
However, this does mean that values 1
and 0
are
no longer converted automatically. They must be specified in
the string arguments, or else the function will report them as
untranslated and converts them to NA
. The same applies
to TRUE
, FALSE
and NA
. Note the
difference between the character string "NA"
and the
value NA
.
Finally, if the imputation-status column contains character
strings, the main QC function QC_GWAS
requires
that all values are translated. If not, QC_GWAS
will
abort the QC.
Examples
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)) )