Description Usage Arguments Details Value Author(s) See Also Examples
View source: R/filter.ampliconduo.set.R
Marks or removes amplicons from each ampliconduo data frame in a list according to the specified filter criteria.
1 |
x |
List of ampliconduo data frames, return value of an |
min.freq |
Optional. Integer, minimium frequency/read count for a given amplicon in each of the two amplicon sets of an ampliconduo 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 ( |
For every ampliconduo
data frame in argument x
, applies
each filter criterion that was specified to each amplicon.
If an amplicon i fails any 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 in respect to the data used as input for the ampliconduo
call are kept.
This method uses the function filter.ampliconduo
.
List of ampliconduo data frames. Same as input parameter x
but with the adjustments in the rejected
column according to the specified filter criteria, or removed rows (removed = TRUE
)
Anja Lange & Daniel Hoffmann
filter.ampliconduo
, performs filtering on single ampliconduo data.frames, is called by this method.
ampliconduo
, generates the input data x
for this method.
accepted.amplicons
, returns the indices of amplicons that
have passed the filter criteria.
1 2 3 4 5 6 7 8 9 10 | ## load example data
data(amplicons)
## apply filter criteria
ampliconduos.f <- filter.ampliconduo.set(amplicons)
ampliconduos.f <- filter.ampliconduo.set(amplicons, min.freq = 3, 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(ampliconduos.f)
|
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