Marr: Marr

In marr: Maximum rank reproducibility

Description

This function applies an Rcpp-based implementation of a computationally efficient method for assessing reproducibility in high-throughput experiments, called the the Marr procedure. This function also defines the Marr class and constructor.

Usage

Marr(object, pSamplepairs = 0.75, pFeatures = 0.75, alpha = 0.05)

Arguments

object	an object which is a matrix or data.frame with features (e.g. metabolites or genes) on the rows and samples as the columns. Alternatively, a user can provide a SummarizedExperiment object and the assay(object) will be used as input for the Marr procedure.
pSamplepairs	(Optional) a threshold value that lies between 0 and 1, used to assign a feature to be reproducible based on the reproducibility output of the sample pairs per feature. Default is 0.75.
pFeatures	(Optional) a threshold value that lies between 0 and 1, used to assign a sample pair to be reproducible based on the reproducibility output of the features per sample pair. Default is 0.75.
alpha	(Optional) level of significance to control the False Discovery Rate (FDR). Default is 0.05.

Details

marr (Maximum Rank Reproducibility) is a nonparametric approach, which assesses reproducibility in high-dimensional biological replicate experiments. Although it was originally developed for RNASeq data it can be applied across many different high-dimensional biological data including MassSpectrometry based Metabolomics and ChIPSeq. The Marr procedure uses a maximum rank statistic to identify reproducible signals from noise without making any distributional assumptions of reproducible signals. This procedure can be easily applied to a variety of measurement types since it employs a rank scale.

This function computes the distributions of percent reproducible sample pairs (row-wise) per feature and percent reproducible features (column-wise) per sample pair, respectively. Additionally, it also computes the percent of reproducible sample pairs and features based on a threshold value. See the vignette for more details.

Value

A object of the class Marr that contains a numeric vector of the Marr sample pairs in the MarrSamplepairs slot, a numeric vector of the Marr features in the MarrFeatures slot, a numeric value of the Marr filtered features in the MarrSamplepairsfiltered slot, and a numeric value of the Marr filtered sample pairs in the MarrFeaturesfiltered slot.

References

Philtron, D., Lyu, Y., Li, Q. and Ghosh, D., 2018. Maximum Rank Reproducibility: A Nonparametric Approach to Assessing Reproducibility in Replicate Experiments. Journal of the American Statistical Association, 113(523), pp.1028-1039.

Examples

data <- matrix(rnorm(2400), nrow=200, ncol=12)
data_Marr <- Marr(object = data, pSamplepairs=0.75,
                  pFeatures=0.75, alpha=0.05)
data("msprepCOPD")
data_Marr_COPD <- Marr(object = msprepCOPD, pSamplepairs=0.75,
                       pFeatures=0.75, alpha=0.05)

marr documentation built on March 10, 2021, 2 a.m.