NEWS.md

In cgplab/PAMES: Purity Assessment from clonal MEthylation Sites

PAMES v3.0.0 aka PAMES2

PAMES has been completely rewritten to work with our new framework MiMeSis Major changes: - all functions now return a data.frame instead of a vector: according to our experience, data.frames integrate better with pipelines; - get_AUC replaces compute_AUC and takes as input a matrix of beta-values as originally produced by Illumina Beadchips (instead of rounded percentages); - find_informative_sites and find_informative_regions replace select_informative_sites and select_informative_regions, respectively, and integrate the new control_constraints parameter; - get_purity replace compute_purity and takes as input a data.frame (generated by find_informative_sites/find_informative_regions).

PAMES v2.7.2

• rename median_of_regions: reduce_region
• add method parameter to reduce_to_regions: allow choice between "median" (default) or mean

PAMES v2.7.1

• fix select_informative_regions_ext with flag return_info=TRUE

PAMES v2.7.0

• renamed parameter platform to ref_table

PAMES v2.5.0

• added new function (select_informative_sites_ext.R) that:
• considers also control data distribution
• use custom platform data (useful to filter out chromosomes X and Y)
• return named vectors (names are either derived from rownames of tumor_data or created with format "CpG_xxxxxxx")
• compute_purity now requires platform data (not just "450k" or "27k") addressing issue#7)

PAMES v2.4.0

• deprecated parameter na_threshold in favor of min_sample_frac compute_AUC
• added simplify parameter: if false return a data.frame reporting fraction of NA samples per site

PAMES v2.3.5

• compute_AUC now returns a vector with the names of the CpG probes.

PAMES v2.3.4

• Add platform parameter to compute_purity to address issue #7)

PAMES v2.3.3

• 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 simpler 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.

cgplab/PAMES documentation built on Dec. 4, 2022, 6:35 p.m.