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Filtering reads on the go!

What if, from all of the reads in a file, you are only interested in some of those reads? You can use a filter!

Let's say that you are interested only in those reads that start with the pattern "ATGCA". A tiny filtering function can do the job, making use of the srFilter() function:

myStartFilter <- srFilter(function(x) substr(sread(x), 1, 5) == "ATGCA")

This function, which has been created for you, takes a ShortRead derived object as an input and outputs the reads starting with the pattern "ATGCA". Let's put this function to use!

Bu egzersiz

Introduction to Bioconductor in R

kursunun bir parçasıdır
Kursu Görüntüle

Uygulamalı interaktif egzersiz

Bu örnek kodu tamamlayarak bu egzersizi bitirin.

# Load package ShortRead
library(ShortRead)

# Check class of fqsample
___

# Filter reads into selectedReads using myStartFilter
selectedReads <- fqsample[___(___)]

# Check class of selectedReads
___
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