filter.ampliconduo {AmpliconDuo} | R Documentation |
AmpliconDuo Amplicon Filter
Description
Marks or removes amplicons from an ampliconduo data frame according to the specified filter criteria.
Usage
filter.ampliconduo(x, min.freq = 1, OR = NULL, q = NULL, p = NULL, remove = FALSE)
Arguments
x |
Data frame, an ampliconduo data frame returned by the |
min.freq |
Optional. Integer, minimium frequency/read count for an amplicon in each of the two amplicon sets to be retained. Default value is 1. |
OR |
Optional. Numeric, minimum odds ratio for an amplicon to be retained. If no value is specified the odds ratio is excluded from the filter criteria. |
q |
Optional. Numeric, minimum value for |
p |
Optional. Numeric, minimum p-value for an amplicon to pass the filter. If no value for |
remove |
Optional. Logical, decides whether amplicons that fail the filter criteria should be removed ( |
Details
Takes the ampliconduo
data frame x
and applies each filter criterion that is selected to each amplicon.
If an amplicon i does not pass each of the applied criteria, the logical value in column rejected
in row i is set to TRUE
.
In case the parameter remove
was set to TRUE
, all amplicons with rejected = TRUE
are removed. The position information with respect to the data used as input for the ampliconduo
call is retained.
Value
Data frame corresponding to the input x
, but with the adjustments in the rejected
column according to the specified filter criteria, or removed rows (removed = TRUE
).
Author(s)
Anja Lange & Daniel Hoffmann
See Also
ampliconduo
, generates the input data x
for this method.
accepted.amplicons
, returns the indices of amplicons that
have passed the filter criteria.
Examples
##load example data
data(amplicons)
## extract the first ampliconduo data frame
ampliconduo1 <- amplicons[[1]]
## apply filter criteria
ampliconduo1.f <- filter.ampliconduo(ampliconduo1)
ampliconduo1.f <- filter.ampliconduo(ampliconduo1, min.freq = 2, remove = TRUE)
## to return a list with the indices (corresponding to the indices of the data
## the ampliconduo function was called on) of all amplicons that passed the filter criteria
good.reads <- accepted.amplicons(ampliconduo1.f)