filter.ampliconduo: AmpliconDuo Amplicon Filter

In AmpliconDuo: Statistical Analysis of Amplicon Data of the Same Sample to Identify Artefacts

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 ampliconduo function.
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 q, the adjusted p-value for an amplicon to pass the filter. If no value is specified, q is excluded from the filter criteria.
p	Optional. Numeric, minimum p-value for an amplicon to pass the filter. If no value for p is specified p is excluded from the filter criteria.
remove	Optional. Logical, decides whether amplicons that fail the filter criteria should be removed (TRUE), or retained (FALSE).

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)

AmpliconDuo documentation built on July 1, 2020, 10:21 p.m.