We now often observe that the genewise filter (cutoff.geneWiseFilter) chosen by BSFind by default is far too high (i.e 0.7-0.9) and then then resulting binding sites do not capture what is seen in IGV.
We should change that. Either by default BSFind should not use the genewise filter or it should default to a low value, like maybe 0.01 or 0.05.
Then the user can still decide to add the genewise filter if necessary.
We now often observe that the genewise filter (
cutoff.geneWiseFilter) chosen by BSFind by default is far too high (i.e 0.7-0.9) and then then resulting binding sites do not capture what is seen in IGV.We should change that. Either by default BSFind should not use the genewise filter or it should default to a low value, like maybe 0.01 or 0.05.
Then the user can still decide to add the genewise filter if necessary.