compareSamples: Sample comparison

In HimesGroup/qmtools: Quantitative Metabolomics Data Processing Tools

Sample comparison

Description

Function to make a comparisons between two groups in study samples with a SummarizedExperiment.

Usage

compareSamples(
  x,
  i,
  group,
  class1,
  class2,
  covariates = NULL,
  confint = TRUE,
  number = nrow(x),
  adjust.method = "BH",
  sort.by = "B",
  resort.by = NULL,
  p.value = 1,
  fc = NULL,
  lfc = NULL,
  ...
)

Arguments

x	A SummarizedExperiment object.
i	A string or integer value specifying which assay values to use. The assay is expected to contain log-transformed intensities.
group	A string specifying the name of variable containing a class label of each sample in colData(x).
class1, class2	A string specifying the class label of samples to be compared. Must be one of group levels. No need to be specified if group has only two levels. This function evaluates the contrast: class2 - class1.
covariates	A vector indicating the names of variables to be included in the model as covariates. The covariates must be found in colData(x).
confint	A logical specifying whether 95% confidence intervals of log-fold-change need to be reported. Alternatively, a numeric value between zero and one specifying the confidence level required.
number	The maximum number of metabolic features to list.
adjust.method	A string specifying which p-value adjustment method to use. Options, in increasing conservatism, include "none", "BH", "BY" and "holm". See p.adjust for the complete list of options. A NULL value will result in the default adjustment method, which is "BH".
sort.by	A string specifying which statistic to rank the metabolic features by. Possible values for topTable are "logFC", "AveExpr", "t", "P", "p", "B" or "none" (Permitted synonyms are "M" for "logFC", "A" or "Amean" for "AveExpr", "T" for "t" and "p" for "P").
resort.by	A string specifying statistic to sort the selected metabolic features by in the output. Possibilities are the same as for sort.by.
p.value	A numeric value specifying a cut-off for adjusted p-values. Only metabolic features with lower p-values are listed.
fc	A numeric value specifying a minimum fold-change to be required. If specified, the function output only includes metabolic features with absolute fold-change greater than fc.
lfc	A numeric value specifying a minimum log-fold-change required. fc and lfc are alternative ways to specify a fold-change cut-off and, if both are specified, then fc take precedence.
...	Additional arguments passed to limma::eBayes.

Details

This function provides a simplified interface of fitting a linear model to make a comparison of interest using the limma::lmFit, limma::eBayes, and limma::topTable functions. For more flexible model specifications (e.g., interaction model, multi-level model), please use a standard workflow outlined in the limma package user's guide.

Value

A data.frame with a row for the metabolic features and the following columns:

• logFC: an estimate of log-fold-change corresponding to the contrast tested

• CI.L: a left limit of confidence interval for logFC (if confint is enabled)

• CI.R: a right limit of confidence interval for logFC (if confint is enabled)

• AveExpr: an average log-expression/abundance of metabolic features

• t: a moderated t-statistic

• P.Value: a raw p-value

• adj.P.Value: an adjusted p-value

• B: a log-odds that the metabolic feature is differentially expressed

References

Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015 Apr 20;43(7):e47. doi: 10.1093/nar/gkv007. Epub 2015 Jan 20. PMID: 25605792; PMCID: PMC4402510.

See Also

See limma::lmFit, limma::eBayes, and limma::topTable for underlying functions that do work.

Examples

data(faahko_se)

compareSamples(faahko_se, i = "knn_vsn", group = "sample_group", number = 5)

HimesGroup/qmtools documentation built on April 16, 2023, 8 p.m.