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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.