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ATAC-seq timewise differential analysis

Source: R/atac_differential_analysis.R
atac_timewise_da.Rd

Use limma to perform pairwise contrasts between each group of trained animals and the sex-matched control group for a single tissue. Analysis is performed separately for males and females.

Usage

atac_timewise_da(
  tissue,
  covariates = c("Sample_batch", "peak_enrich.frac_reads_in_peaks.macs2.frip"),
  outliers = data.table::data.table(MotrpacRatTraining6moData::OUTLIERS)[assay == "ATAC",
    viallabel],
  scratchdir = ".",
  rdata_outfile = NULL,
  overwrite = FALSE,
  verbose = TRUE,
  n_features = Inf
)

Arguments

tissue

character, tissue abbreviation, one of MotrpacRatTraining6moData::TISSUE_ABBREV

covariates

character vector of covariates that correspond to column names of MotrpacRatTraining6moData::ATAC_META. Defaults to covariates that were used for the manuscript.

outliers

vector of viallabels to exclude during differential analysis. Defaults to OUTLIERS$viallabel

scratchdir

character, local directory in which to download data from Google Cloud Storage. Current working directory by default.

rdata_outfile

NULL or path in which to save eBayes objects in an RData file

overwrite

boolean, whether to overwrite the file if rdata_outfile exists

verbose

boolean, whether to print messages

n_features

integer, number of peaks to perform differential analysis on. Useful for troubleshooting.

Value

a data frame with one row per feature:

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'

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.

covariates

character, comma-separated list of adjustment variables

removed_samples

character, comma-separated list of outliers (vial labels) removed from differential analysis

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

p_value

double, unadjusted p-value for the difference between 'comparison_group' and the group of sex-matched sedentary control animals

Examples

if (FALSE) {
# Perform timewise differential analysis for chromatin accessibility peaks 
# measured in hippocampus with default parameters.
hippoc_atac_da = atac_timewise_da("HIPPOC")
}