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MANO-B / MicroSEC

MicroSEC filtering pipeline for FFPE artifacts
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fun_load_mutation() causes error when `-` s are set for SimpleRepeat_TRF (bafbaa1 (2.1.5)) #4

Open monagai opened 4 weeks ago

monagai commented 4 weeks ago

It seems that simple_repeat_info <- read.csv(simple_repeat_list...) in fun_load_mutation() causes error when - s are set for SimpleRepeat_TRF (bafbaa1 (2.1.5)). Because simple_repeat_list is not an argument of fun_load_mutation() and fun_load_mutation() initializes it as NULL, simple_repeat_list is always NULL (and "simple_repeat_list" %in% ls()" is always TRUE) in fun_load_mutation().

P.S. install.packages(c('stringr', 'tidyverse', 'remotes'), dependencies = TRUE) would be better than install.packages(c('stringr', 'dplyr', 'remotes'), dependencies = TRUE) in README.

MANO-B commented 3 weeks ago

We thank you very much for kindly pointing out the problems, including how to improve them. We updated the package, document, and docker file.

monagai commented 3 weeks ago

It's my pleasure. I really thank you for your quick response. I think MicroSEC is quite useful for FFPE data.