clean.data: clean.data

In PAIRADISE: PAIRADISE: Paired analysis of differential isoform expression

Description

Removes missing data and invalid pairs from the matched pair data to be analyzed by PAIRADISE.

Usage

clean.data(my.data)

Arguments

my.data

Data frame containing grouped data to be analyzed.

Details

The data frame has 7 columns, arranged as follows: Column 1 contains the ID of the exons/events. Column 2 contains counts of isoform 1 corresponding to the first group. Column 3 contains counts of isoform 2 corresponding to the first group. Column 4 contains counts of isoform 1 corresponding to the second group. Column 5 contains counts of isoform 2 corresponding to the second group. Replicates in columns 2-5 should be separated by commas, e.g. 1623,432,6 for three replicates. Column 6 contains the effective length of isoform 1. Column 7 contains the effective length of isoform 2.

Value

The function clean.data returns a list containing the following entries:

I1	Group 1 isoform 1 counts for each replicate.
S1	Group 1 isoform 2 counts for each replicate.
I2	Group 2 isoform 1 counts for each replicate.
S2	Group 2 isoform 2 counts for each replicate.
length_I	Effective lengths of isoform 1.
length_S	Effective lengths of isoform 2.
exonList	IDs of the exons/events.
nExon	Number of exons/events.
M	Vector containing the number of replicates per exon/event.

PAIRADISE documentation built on Nov. 8, 2020, 8:22 p.m.