remove_0_1_pA_transcripts: remove_0_1_pA_transcripts

In goodarzilab/APAlog: Analysis of alternative poly A site usage

remove_0_1_pA_transcripts

Description

Function to remove transcripts with fewer than two active pA sites from dataset

Usage

remove_0_1_pA_transcripts(data)

Arguments

data

Dataset containing poly A (pA) site read counts. This dataset must have a long shape, meaning that there should be only one column containing read counts (and it MUST be named "count"). The first four columns must be called "transcript", "pA.site", "sample" and "count". Thus, each row in data contains the read count for one pA - transcript - sample combination. Other sample attributes beyond sample ID may be recorded in additional variables in this dataset, or provided separately through a design matrix and a key variable (e.g. sample ID) connecting the data and design matrices.

Details

This function counts the number of pA sites with non-zero read counts for each transcripts and removes transripts with fewer than two active pA sites. This is essential to avoid errors when running the regression models.

Value

A subset of the input dataset where all transcripts are guaranteed to have two or more active pA sites.

goodarzilab/APAlog documentation built on March 25, 2022, 3:40 p.m.