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colomemaria / epiAneufinder

R package to detect breakpoints and assign somies to scATAC-seq data
GNU General Public License v3.0
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results_table.tsv rows are not the same size in multiple samples #4

Closed tinakeshav closed 2 years ago

tinakeshav commented 2 years ago

Hi epiAneufinder devs, Thank you for releasing such an easy-to-use package. I've used this package for multiple samples and the results_table.tsv data frame does not have the same number of rows for every sample. Initially I thought it's not saving rows that are all state 1 (normal), but there are rows in some samples that are only state 1. Could you kindly elaborate on why the row number of results_table.tsv differ from each other? Thank you so much!

akshaya4r commented 2 years ago

Hi tinakeshav, For each sample, bins that have 0 counts in 85% or more of the population are removed such that the CNV calls aren't affected by other biases. This is why you could have different number of rows in the results table.