Package: qmtools 1.17.0

Jaehyun Joo

qmtools: Quantitative Metabolomics Data Processing Tools

The qmtools (quantitative metabolomics tools) package provides basic tools for processing quantitative metabolomics data with the standard SummarizedExperiment class. This includes functions for imputation, normalization, feature filtering, feature clustering, dimension-reduction, and visualization to help users prepare data for statistical analysis. This package also offers a convenient way to compute empirical Bayes statistics for which metabolic features are different between two sets of study samples. Several functions in this package could also be used in other types of omics data.

Authors:Jaehyun Joo [aut, cre], Blanca Himes [aut]

qmtools_1.17.0.tar.gz
qmtools_1.17.0.zip(r-4.7)qmtools_1.17.0.zip(r-4.6)qmtools_1.17.0.zip(r-4.5)
qmtools_1.17.0.tgz(r-4.6-any)qmtools_1.17.0.tgz(r-4.5-any)
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
qmtools/json (API)

# Install 'qmtools' in R:

install.packages('qmtools', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/himesgroup/qmtools/issues

Datasets:

faahko_se - FAAH knockout LC/MS data SummarizedExperiment

On BioConductor:qmtools-1.17.0(bioc 3.24)qmtools-1.16.0(bioc 3.23)

metabolomics preprocessing normalization dimensionreduction massspectrometry

4.72 score 2 stars 13 scripts 334 downloads 22 exports 178 dependencies

Last updated from:d6a8cbea41. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	216
linux-devel-x86_64	NOTE	406
source / vignettes	OK	298
linux-release-x86_64	NOTE	348
macos-release-arm64	NOTE	222
macos-oldrel-arm64	NOTE	177
windows-devel	NOTE	600
windows-release	NOTE	242
windows-oldrel	NOTE	600
wasm-release	OK	189

Exports:clusterFeatures compareSamples imputeIntensity imputeKNN normalizeIntensity normalizePQN plotBox plotCorr plotMiss plotReduced plotRTgroup reduceFeatures reducePCA reducePLSDA reduceTSNE removeBlankRatio removeFeatures removeICC removeMiss removeRSD scaleCols scaleRows

Dependencies:abind askpass assertthat backports base64enc bbotk Biobase BiocGenerics boot broom bslib ca cachem callr car carData checkmate class cli clue cluster codetools colorspace cowplot cpp11 crosstalk curl data.table DelayedArray dendextend DEoptimR Deriv digest doBy dplyr e1071 egg evaluate farver fastmap fontawesome foreach forecast Formula fracdiff fs future future.apply gclus generics GenomicRanges ggplot2 globals glue gridExtra gtable heatmaply highr htmltools htmlwidgets httr igraph IRanges isoband iterators jquerylib jsonlite knitr labeling laeken later lattice lazyeval lgr lifecycle limma listenv lme4 lmtest magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mgcv microbenchmark mime minqa mirai mlbench mlr3 mlr3learners mlr3measures mlr3misc mlr3pipelines mlr3tuning modelr MsCoreUtils nanonext nlme nloptr nnet numDeriv openssl otel palmerpenguins paradox parallelly patchwork pbkrtest permute pillar pkgconfig plotly plyr processx promises proxy PRROC ps purrr qap quantreg R6 ranger rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack reformulas registry reshape2 rlang rmarkdown robustbase S4Arrays S4Vectors S7 sass scales Seqinfo seriation sp SparseArray SparseM statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect timeDate tinytex TSP urca utf8 uuid vcd vctrs vegan VIM viridis viridisLite webshot withr xfun xgboost XVector yaml zoo

Processing quantitative metabolomics data with the qmtools package

Rendered fromqmtools.Rmdusingknitr::rmarkdown

Last update: 2023-04-02
Started: 2022-03-17

Help page	Topics
Feature clustering	clusterFeatures
Sample comparison	compareSamples
FAAH knockout LC/MS data SummarizedExperiment	faahko_se
Imputation methods	imputeIntensity imputeIntensity,ANY-method imputeIntensity,SummarizedExperiment-method
k-nearest neighbor imputation	imputeKNN
Normalization methods	normalizeIntensity normalizeIntensity,ANY-method normalizeIntensity,SummarizedExperiment-method
Probabilistic quotient normalization (PQN)	normalizePQN
Box plot	plotBox
Correlation plot	plotCorr
Missing value plot	plotMiss
Score plot of dimension-reduced data	plotReduced
Helper to visualize feature grouping	plotRTgroup
Dimension reduction methods	reduceFeatures reduceFeatures,ANY-method reduceFeatures,SummarizedExperiment-method
Principal component analysis (PCA)	reducePCA
Partial least squares-discriminant analysis (PLS-DA)	reducePLSDA
t-distributed stochastic neighbor embedding (t-SNE)	reduceTSNE
Feature Filtering based on QC/blank ratio	removeBlankRatio
Feature Filtering methods	removeFeatures removeFeatures,ANY-method removeFeatures,SummarizedExperiment-method
Feature Filtering based on ICC	removeICC
Feature filtering based on proportions of missing values	removeMiss
Feature Filtering based on RSD	removeRSD
Scale along columns (samples)	scaleCols
Scale along rows (features)	scaleRows

Package: qmtools 1.17.0

qmtools: Quantitative Metabolomics Data Processing Tools

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