methylKit
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al2na
switch to iotools for chunkwise apply
There is this nice package iotools (https://cran.r-project.org/web/packages/iotools/iotools.pdf) which allows fast chunkwise reading and writing from files. It supports connections, i.e. can read and write from /to gzipped files directly. It has some apply functionality build in which could become handy for our applyByTabix functions.
Iotools or fread then? How well is this maintained? Can we depend on them for the long-run?
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On Tue, Feb 5, 2019, 10:06 AM Alexander Gosdschan <[email protected] wrote:
There is this nice package iotools ( https://cran.r-project.org/web/packages/iotools/iotools.pdf) which allows fast chunkwise reading and writing from files. It supports connections, i.e. can read and write from /to gzipped files directly. It has some apply functionality build in which could become handy for our applyByTabix functions.
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Iotools or fread then?
I would use both, because fread determines column types automatically and still can read content very fast into memory.
How well is this maintained? Can we depend on them for the long-run?
It is there since R2.9 and is serving only the purpose of streaming files, so probably well tested for this. I does actually only have two depending packages, but itself has no other dependencies than R.
ok, sounds promising.
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On Tue, Feb 5, 2019, 10:30 AM Alexander Gosdschan <[email protected] wrote:
Iotools or fread then?
I would use both, because fread determines column types automatically and still can read content very fast into memory.
How well is this maintained? Can we depend on them for the long-run?
It is there since R2.9 and is serving only the purpose of streaming files, so probably well tested for this. I does actually only have two depending packages, but itself has no other dependencies than R.
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