clones.filterSize: Filter clones for their size
In bcRep: Advanced Analysis of B Cell Receptor Repertoire Data

Description Usage Arguments Details Value Author(s) See Also Examples

This function filters clones for their size (clone copy number). It can be filtered for different kinds of tresholds (see Details).

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clones.filterSize(clones.tab = NULL, column = NULL, number = NULL, 
     propOfClones = NULL, propOfSequences = NULL, 
     method = c("two.tailed", "upper.tail", "lower.tail"))

`clones.tab`	A data frame containing clones and their characteristics
`column`	Name or number of column to be filtered
`number`	An integer, giving treshold for size
`propOfClones`	A proportion between 0 and 1, giving proportion of all clones (see Details)
`propOfSequences`	A proportion between 0 and 1, giving proportion of all sequences (see Details)
`method`	Filter method, either smallest and biggest numbers, only smallest or only biggest numbers (see Details)

This function filters clones for their size (clone copy number; total number of sequences belonging to a clone). It can be filtered for

1) a given number of sequences, e.g. number=20: the 20 biggest and/or 20 smallest clones,

2) a proportion of all clones, e.g. propOfClones=0.2: the 20% biggest and/or smallest clones,

3) a proportion of all sequences, e.g. propOfSequences=0.01: Clones, were more and/or less than 1% of all sequences are included.

Only of these criteria is required.

Method determines which clones shall be returned: 1) biggest and smallest clones (two.tailed), 2) biggest clones (upper.tail) or 3) smallest clones (lower.tail). In case of two.tailed a list containing upper and lower tail will be returned.

Ouput is a data frame (upper.tail, lower.tail) or a list (two.tailed), containing filtered clones.

Julia Bischof

clones.filterFunctionality, clones.filterJunctionFrame

data(clones.ind)

clones.filtered1<-clones.filterSize(clones.tab=clones.ind, 
     column="total_number_of_sequences", number=20, method="two.tailed")
clones.filtered2<-clones.filterSize(clones.tab=clones.ind, column=4, propOfClones=0.1, 
     method="upper.tail")
clones.filtered3<-clones.filterSize(clones.tab=clones.ind, column=4, 
     propOfSequences=0.02, method="lower.tail")