NEWS.md

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.