Proteomics timewise differential analysis — proteomics_timewise

Timewise differential analysis for the proteome, phosphoproteome, acetylome, and ubiquitylome. Use limma to perform pairwise contrasts between each group of trained animals and the sex-matched control group for a single tissue and proteomics assay. Analysis is performed separately for males and females.

Usage

proteomics_timewise_da(assay, tissue, exclude_outliers = TRUE)

Arguments

assay: character, abbreviation for proteomics assay to be analyzed as defined by MotrpacRatTraining6moData::ASSAY_ABBREV. One of the following: PROT, PHOSPHO, ACETYL, UBIQ
tissue: character, tissue abbreviation, one of MotrpacRatTraining6moData::TISSUE_ABBREV
exclude_outliers: bool, whether to remove sample outliers specified in MotrpacRatTraining6moData::OUTLIERS. TRUE by default.

Value

a data frame with one row per proteomics feature per contrast (usually 8 rows 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.
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
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
numNAs: integer, number of missing values in the current 'comparison_group' and sex-matched sedentary control animals

Examples

# Run timewise differential analysis for heart proteins
res = proteomics_timewise_da("PROT","HEART")
#> PROT_HEART_NORM_DATA