clones.filterSize: Filter clones for their size

Description

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

Usage

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

Arguments

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)

Value

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

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.

Examples

Run this code

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")