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).

1 2 3 |

`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`

1 2 3 4 5 6 7 8 | ```
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")
``` |

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