Need information on how filterAndTrim function from the DADA2 pipeline was developed

Question

[Akshay]

Hi Everyone,

I am looking for the basic code that was compiled to build the function "filterAndTrim" from the DADA2 pipeline (https://benjjneb.github.io/dada2/tutorial.html). In the documentation for the filterAndTrim function (https://rdrr.io/bioc/dada2/man/filterAndTrim.html), it was mentioned that filterAndTrim is a multithreaded convenience interface for the fastqFilter and fastqPairedFilter filtering functions.

But, I am looking for more basic answers like

1) In what language is the basic code of this function (C++ or R)?

2) Secondly, what is the basic code of this function? I want to see how it is programmed.

Thank you.

[Akshay]

Thank you GenoMax AND Philipp Bayer

[Akshay]

I had a follow-up question, how to I redefine the same function, so that instead of giving each argument a value, I can input a iterative list of values.

for example: instead of truncLen=c(240,160), I want to input truncLen=c(forward_param,reverse_param), in which forward_param is a loop of 180, 200, 220, 240, 260 and reverse_param is also a loop of 180, 200, 220, 240, 260.

or instead of maxEE=c(2,2), I want to input maxEE=c(x,y), in which x is a loop of 1, 2, 3, 4, 5 and y is also a loop of 1, 2, 3, 4, 5.

.... so and so for each argument.

[GenoMax]

Please ask a separate question since this is not directly related to the original thread.

Answer 1

[GenoMax]

You can find the source code links on https://www.bioconductor.org/packages/release/bioc/html/dada2.html. Scroll down to "Package archive" section.

[Philipp Bayer]

or on Github: https://github.com/benjjneb/dada2/blob/e0029d098151e0f33ae482a061d388ada4f15fdb/R/filter.R#L402