How to overcome R memory error

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3.8 years ago

2405592M ▴ 140

My R script keeps returning the following error:

Error in readLines(file) : R character strings are limited to 2^31-1 bytes

Clearly, my input fasta files are too big. What is the best way around this problem. I initially thought I'd have to convert this segment of the script into python, but I was hoping to find an R-based solution first.

RNA-Seq FASTA R • 1.9k views

ADD COMMENT • link 3.8 years ago by 2405592M ▴ 140

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Can you explain what you are trying to do. Code alone without any comments is not appropriate as a question.

ADD REPLY • link 3.8 years ago by ATpoint 81k

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The script calculates the relative synonymous codon usage of transcript coding sequences (these are the input fasta files). The first step converts the input fasta file into character strings (which is required for the uco function) and I think that is the origin of the error.

ADD REPLY • link 3.8 years ago by 2405592M ▴ 140

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Are you sure you are reading in a transcripts fasta? I can't think of a gene coding region being this long.

ADD REPLY • link 3.8 years ago by h.mon 35k

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