Differential analysis results of RRBS data — METHYL

Timewise summary statistics and training FDR from differential analysis (DA) that tests the effect of training on each methylation feature within each sex. One data frame per tissue.

Format

A data frame with 20 variables:

feature: character, unique feature identifier in the format 'ASSAY_ABBREV;TISSUE_ABBREV;feature_ID' only for training-regulated features at 5% IHW FDR. For redundant differential features, 'feature_ID' is prepended with the specific platform to make unique identifiers. See REPEATED_FEATURES for details.
assay: character, assay abbreviation, one of ASSAY_ABBREV
assay_code: character, assay code used in data release. See MotrpacBicQC::assay_codes.
tissue: character, tissue abbreviation, one of TISSUE_ABBREV
tissue_code: character, tissue code used in data release. See MotrpacBicQC::bic_animal_tissue_code.
feature_ID: character, MoTrPAC feature identifier
sex: character, one of 'male' or 'female'
comparison_group: character, time point of trained animals compared to the sex-matched sedentary control animals, one of '1w', '2w', '4w', '8w'
p_value: double, unadjusted p-value for the difference between 'comparison_group' and the group of sex-matched sedentary control animals
adj_p_value: double, adjusted p-value from 'p_value' column. P-values are BY-adjusted across all datasets within a given assay/ome.
logFC: double, log fold-change where the numerator is 'comparison_group', e.g., '1w', and the denominator is the group of sex-matched sedentary control animals
zscore: double, z statistic
covariates: character, comma-separated list of adjustment variables or NA
removed_samples: character, comma-separated list of vial labels excluded from differential analysis or NA
Chr: integer, chromosome
Locus: character, base pair range of feature
EntrezID: character, Entrez ID of closest gene
Symbol: character, gene symbol of closest gene
fscore: numeric, F-score
selection_fdr: double, adjusted training p-value used to select training-regulated analytes. P-values are IHW-adjusted across all datasets within a given assay with tissue as a covariate.

Details

Unfiltered METHYL differential analysis results are only available via download from Google Cloud Storage. For example, https://storage.googleapis.com/motrpac-rat-training-6mo-extdata/epigen-rda/METHYL_BAT_DA.rda is the file for brown adipose tissue (BAT) results. You can change the name of the file to specify other tissues including: HEART, HIPPOC, KIDNEY, LIVER, LUNG, SKMGN (gastrocnemius skeletal muscle), and WATSC (subcutaneous white adipose tissue). You can also use MotrpacRatTraining6mo::get_rdata_from_url() to download differential analysis results for ATAC and METHYL. For more details about these files see the readme of this repository at https://github.com/MoTrPAC/MotrpacRatTraining6mo/blob/main/README.md.

The differential analysis results in this data frame were computed using edgeR::glmQLFTest() after removing a few outlier low quality samples from the kidney dataset.

For training-regulated METHYL features at 5% FDR, see TRAINING_REGULATED_FEATURES.

Reproduce our analysis with MotrpacRatTraining6mo::rrbs_differential_analysis().