Fixed bugs that caused addWeights to fail when aggregateCells = TRUE.
When aggregateCells is set to TRUE, cells are aggregated by calculating the mean of the original cell features rather than their sums.
Fixed a warning about the class of the cellNum argument passed to calculateP2G, which was raised incorrectly.
optimizeMatacellNumber, which estimates the optimal value of the cellNum parameter
passed to calculateP2G.scrapper::clusterKmeans to implement deterministic algorithm of determination k-mean cluster.
It is used to create metacells in the calculateP2G function.calculateP2G function empirical p-values and FDR. The null distribution
is calculated based on random links of peaks to the genes from other chromosomes.tfBinding is changed to version 2 which imposes more stringent cutoffs.
We have increased the number of unique reads to 20M (previously 10M in version 1) and the number of peaks passing
FDR < 1e-5 to 1000 peaks (previously 100 peaks in version 1). For ENCODE data, we now remove any samples with
Audit.NOT_COMPLIANT or Audit.ERROR. Flags.method to calculateActivity has been deprecated.addLogFC. p-values were mistakenly transformed from log10 when it should be transformed from natural log
when logFC_ref or/and logFC_condition was specifiedaddMotifScore returns correct values instead of NA.aggregateAcrossCellsFast has been added.aggregateAcrossCells has been added, which is implemented in c++ and makes
run time for calculateP2G much shorter.addLogFC which adds log fold changes of gene expression to regulons and significance statistics for differential gene expressioncellNum argument to calculateP2G set by default to 100 (previously it was 200).pruneRegulon the check to the uniqueness of gene names has been added.Version number downgraded to 0.99.0 to meet Bioconductor requirements.
commit 12fabd3278b76711f4b2cbdcaca6794a918ffd83
addMotifScore function (human_pwms_v1, and mouse_pwms_v1) were replaced wih the new ones (human_pwms_v2, mouse_pwms_v2) which are up-to-date.BUG FIX
clusters vector provided to the addWeights and pruneRegulon functions is checked for the presence of NA values. If they are present the function stops preventing segmentation fault and session abortion.calculateP2G staring position of the gene has been corrected.