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roblanf / sangeranalyseR

functions to analyse sanger sequencing reads in R
MIT License
95 stars 24 forks source link

Change documentation for function args? #73

Closed odcambc closed 2 years ago

odcambc commented 2 years ago

Thanks for the very useful package! I was having a bit of trouble following the examples in the readme and the documentation before I realized that the function calls had changed, though.

Right now the following example is given in the readme:

ACHLO_contigs <- SangerAlignment(ABIF_Directory     = parentDir,
                                 REGEX_SuffixForward = "_[0-9]*_F.ab1$",
                                 REGEX_SuffixReverse = "_[0-9]*_R.ab1$")

This throws an "unused arguments" error. I gather the parameter names have changed. The following works for me:

ACHLO_contigs <- SangerAlignment(parentDirectory     = parentDir,
                                 suffixForwardRegExp = "_[0-9]*_F.ab1$",
                                 suffixReverseRegExp = "_[0-9]*_R.ab1$")

The current version of the beginner's and quick start guides also do not run as written: changing parameter names seems to work, though.

Kuanhao-Chao commented 2 years ago

Hi @odcambc ,

I think the sangeranalyseR that you installed is the the old version. Please reinstall sangeranalyseR again and I think it will work. Here is the installation page.

Howard