combine_feature_intensities: Combine feature intensities of several spectra

In szymczak-lab/preprocessHighResMS: Preprocessing of spectra data from high resolution mass spectrometry

Description

Load extracted information about features such as intensities, peak detection and measured mz values and combine them with phenotype information into a RangedSummarizedExperiment-class object. Features are removed if they have missing mz values or intensities for all samples or constant intensity across all samples.

Usage

combine_feature_intensities(
  feature.files,
  id.samples = NULL,
  pheno = NULL,
  cor.cutoff = 0.9,
  verbose = FALSE
)

Arguments

feature.files	Character vector. Names of files with feature intensities as generated by extract_feature_intensity.
id.samples	Character vector. Identifiers of each file. If NULL, ids will be identified as basenames of files.
pheno	data.frame. Information about each sample. Rownames need to correspond to id.samples. If NULL, pheno will only contain ids.
cor.cutoff	Numeric. Cutoff of the pair-wise absolute correlation (default: 0.9).
verbose	Logical. Print out additional information.

Value

RangedSummarizedExperiment-class object.

Examples

data("info.features")
res.dir = tempdir()
mzml.files = dir(system.file("extdata",
                             package = "preprocessHighResMS"),
                 full.names = TRUE)

sapply(mzml.files,
       extract_feature_intensity,
       scanrange = c(1, 2),
       info.features = info.features,
       ppm = 20,
       res.dir = res.dir)

feature.files = dir(path = res.dir,
                    pattern = ".rds",
                    full.names = TRUE)
se.example = combine_feature_intensities(feature.files = feature.files,
                                         verbose = TRUE)

szymczak-lab/preprocessHighResMS documentation built on Oct. 6, 2020, 12:50 a.m.