PAMES v2.3.2

Fix bug in reduce_to_regions (see issue #6)

PAMES v2.3.1

Fix bug in compute_AUC

PAMES v2.3.0

Add percentiles parameter for a more flexible selection of sites

PAMES v2.2.0

Even faster cluster reduction
Fix bug: "top" method retrieved same sites of "hyper"

PAMES v2.1.0

Faster and simplier cluster reduction in select_informative_sites
Removed internal functions:
- is_too_close
- cluster_reduction
Added variable method to select_informative_sites and select_informative_regions to select even, top, hyper or hypo methylated sites.

PAMES v2.0.0

PAMES have been rewritten to make the code simpler and the analysis run faster. Thanks to GMFranceschini for suggesting to use GenomicRanges.
Removed function:
- compute_islands_indexes.R
Renamed functions:
- reduce_to_islands.R -> reduce_to_regions.R
Renamed data:
- cpg_islands_df -> cpg_islands
Removed data:
- bs_toy_indexes

PAMES v1.1.0

BUG correction: setting na_threshold to be greater than 1 didn't generate an error (and resulted as having na_threshold set to 0.99)

PAMES v1.0.1

Faster compute_AUC thanks to Wilcoxon method

PAMES v1.0.0

New Features

Added parallel computation to compute_AUC with argument ncores.

Updated dataset

cpg_islands has been renamed as cpg_islands_df
bs_tumor_toy_data and bs_control_toy_data has been merged into bs_toy_matrix

Changed behaviour

All beta tables are now required to be percentage values.