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base repository: bharathananth/compareRhythms
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head repository: RSC-RP/compareRhythms
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  • 6 commits
  • 2 files changed
  • 1 contributor

Commits on Nov 3, 2023

  1. Correct the phase calculation

    @lvclark
    lvclark committed Nov 3, 2023
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Commits on Nov 6, 2023

  1. Merge pull request #1 from RSC-RP/patch1 

    Correct the phase calculation
    @lvclark
    lvclark authored Nov 6, 2023

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    Learn about vigilant mode
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  2. Output P-values for cosinor method

    @lvclark
    lvclark committed Nov 6, 2023
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Commits on Jun 18, 2024

  1. Revert to using cosine curve rather than sine curve

    @lvclark
    lvclark committed Jun 18, 2024
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  2. Don't filter results based on rhythmicity

    @lvclark
    lvclark committed Jun 18, 2024
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  3. Typo

    @lvclark
    lvclark committed Jun 18, 2024
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Showing with 7 additions and 3 deletions.
  1. +1 −1 DESCRIPTION
  2. +6 −2 R/compareRhythms_cosinor.R
2 changes: 1 addition & 1 deletion DESCRIPTION
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
Package: compareRhythms
Type: Package
Title: Approaches to identify Differential Rhythmicity
Version: 1.0.2
Version: 1.0.3
Author: Bharath Ananthasubramaniam
Maintainer: Bharath Ananthasubramaniam <bharath.ananthasubramaniam@hu-berlin.deu>
Description: This package identifies features that have altered rhythms
8 changes: 6 additions & 2 deletions R/compareRhythms_cosinor.R
View file
Original file line number Diff line number Diff line change
@@ -82,10 +82,12 @@ compareRhythms_cosinor <- function(data, exp_design, period, rhythm_fdr,
results$max_amp <- pmax(results[, paste0(group_id[1], "_amp")],
results[, paste0(group_id[2], "_amp")])

results$p_val_A_or_B <- rhythmic_in_either

results$adj_p_val_A_or_B <- adj_pval

results <- results[(results$adj_p_val_A_or_B < rhythm_fdr) &
(results$max_amp >= amp_cutoff), ]
# results <- results[(results$adj_p_val_A_or_B < rhythm_fdr) &
# (results$max_amp >= amp_cutoff), ]

assertthat::assert_that(assertthat::not_empty(results),
msg = "Sorry no rhythmic genes in either dataset for the thresholds provided.")
@@ -101,6 +103,8 @@ compareRhythms_cosinor <- function(data, exp_design, period, rhythm_fdr,

diff_rhy_results <- diff_rhy_results[results$id]

results$p_val_DR <- diff_rhy_results

results$adj_p_val_DR <- stats::p.adjust(diff_rhy_results,
method = "BH")
results$diff_rhythmic <- results$adj_p_val_DR < compare_fdr