Combine differential analysis results — combine_da

Combine differential analysis results from the specified tissues and omes(s)/assay(s). If no tissues or omes are specified, all differential analysis results are returned.

Usage

combine_da_results(
  tissues = MotrpacRatTraining6moData::TISSUE_ABBREV,
  assays = MotrpacRatTraining6moData::ASSAY_ABBREV,
  metareg = TRUE,
  include_epigen = FALSE,
  scratchdir = "."
)

Arguments

tissues: optional character vector of tissue abbreviations, one of MotrpacRatTraining6moData::TISSUE_ABBREV.
assays: optional character vector of assay abbreviations, one of MotrpacRatTraining6moData::ASSAY_ABBREV
metareg: bool, whether to use the meta-regression results for METAB. Use the upstream differential analysis results if FALSE. TRUE by default.
include_epigen: bool, whether to include the full ATAC or METHYL differential analysis results from Google Cloud Storage. Only relevant if assays includes "ATAC" or "METHYL". FALSE by default.
scratchdir: character, local directory in which to download data from the web. Current working directory by default. Only relevant if assays includes "ATAC" or "METHYL".

Value

data frame. Depending on the specified assays, some of these columns may not be included:

feature: character, unique feature identifier in the format 'MotrpacRatTraining6moData::ASSAY_ABBREV;MotrpacRatTraining6moData::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 MotrpacRatTraining6moData::REPEATED_FEATURES for details.
assay: character, assay abbreviation, one of MotrpacRatTraining6moData::ASSAY_ABBREV
assay_code: character, assay code used in data release. See MotrpacBicQC::assay_codes.
tissue: character, tissue abbreviation, one of MotrpacRatTraining6moData::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
logFC_se: double, standard error of the log fold-change
tscore: double, t statistic
covariates: character, comma-separated list of adjustment variables or NA
numNAs: integer, number of missing values in the current 'comparison_group' and sex-matched sedentary control animals
comparison_average_intensity: double, average intensity among the replicates in 'comparison_group'
reference_average_intensity: double, average intensity among the replicates in the group of sex-matched sedentary control animals
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.
dataset: character, immune panel, metabolomics platform, or ATAC-seq dataset name
site: character, Chemical Analysis Site (CAS) name. METAB only
is_targeted: logical, is this a targeted platform? METAB only
metabolite_refmet: character, RefMet name of metabolite. METAB only
cv: double, feature coefficient of variation in the dataset. METAB only
metabolite: character, name of metabolite as appears in the CAS's data. METAB only
control_cv: double, feature coefficient of variation in the dataset. METAB only
mz: double, mass over charge. METAB only
rt: double, retention time. METAB only
neutral_mass: double, neutral mass. METAB only
meta_reg_het_p: double, for metabolites with multiple measurements, the meta-regression heterogeneity p-value, where a smaller p-value indicates more disagreement between platforms. One value per feature (not per training group). METAB only
meta_reg_pvalue: double, for metabolites with multiple measurements, the meta-regression p-value. One value per feature (not per training group). METAB only
shrunk_logFC: double, log fold-change with shrinkage applied
shrunk_logFC_se: double, standard error of the shrunken log fold-change
zscore: double, z statistic
removed_samples: character, comma-separated list of vial labels excluded from differential analysis or NA
comparison_average_intensity_se: double, standard error of 'comparison_average_intensity'
reference_average_intensity_se: double, standard error of 'comparison_average_intensity'
Chr: integer, chromosome. METHYL only
Locus: character, base pair range of feature. METHYL only
EntrezID: character, Entrez ID of closest gene. METHYL only
Symbol: character, gene symbol of closest gene. METHYL only

Examples

if (FALSE) { # \dontrun{
# Return all non-epigenetic differential analysis results, 
# including meta-regression results for metabolomics
data = combine_da_results()

# Return all global proteomics differential analysis results
data = combine_da_results(assays="PROT")

# Return METHYL and ATAC differential analysis results for gastrocnemius 
data = combine_da_results(tissues="SKM-GN", 
                          assays=c("ATAC","METHYL"),
                          include_epigen=TRUE)
} # }