Altuna Akalin

could we also comment the code wherever possible, please think about people who will maintain this in the future or your future selves. Certain things that are trivial are not...

please check datasets that have multiple chromosomes lets say at least 5 chromosomes, compare also memory consumption. On Wed, Jul 4, 2018 at 10:55 AM katwre wrote: > I checked...

a correlation matrix is already returned. You need to assign the output of the function to a variable On Fri, Oct 25, 2019 at 1:49 PM tmms1 wrote: > Hello...

OK, this is something we should fix. But getting the correlation matrix is a oneliner `cor.mat = cor(percMethylation(methBase))` let me know if this works

How did you create this methylation call file? The coordinates seem wrong. Forward and reverse strands can't have a cytosine in the same position On Wed, Aug 12, 2020 at...

you have to recreate the S4 object that contains the data frame and other required elements properly then you can use it on downstream analysis. https://github.com/al2na/methylKit/blob/master/R/backbone.R#L1449 On Thu, Aug 19,...

PC2 seems to be associated with the batch, see if removing that helps with the clustering. You can also use the batch as a covariate during differential methylation calculation. Best,...

this could be useful yes, would you like to do a PR? also any ideas on how to return the calculated affect sizes without breaking the object structure and downstream...

Iotools or fread then? How well is this maintained? Can we depend on them for the long-run? from mobile On Tue, Feb 5, 2019, 10:06 AM Alexander Gosdschan There is...

ok, sounds promising. from mobile On Tue, Feb 5, 2019, 10:30 AM Alexander Gosdschan Iotools or fread then? > > I would use both, because fread determines column types automatically...