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, f.e. number=20: the 20 biggest and/or 20 smallest clones,

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

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

Only of of these criteria is required.

Method represents, if 1) biggest and smallest clones (two.tailed), 2) biggest clones (upper.tail) or 3) smallest clones (lower.tail) be returned. 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")