Package: hdxmsqc 1.3.0

Oliver M. Crook

hdxmsqc: An R package for quality Control for hydrogen deuterium exchange mass spectrometry experiments

The hdxmsqc package enables us to analyse and visualise the quality of HDX-MS experiments. Either as a final quality check before downstream analysis and publication or as part of a interative procedure to determine the quality of the data. The package builds on the QFeatures and Spectra packages to integrate with other mass-spectrometry data.

Authors:Oliver M. Crook [aut, cre]

hdxmsqc_1.3.0.tar.gz
hdxmsqc_1.3.0.zip(r-4.5)hdxmsqc_1.3.0.zip(r-4.4)hdxmsqc_1.3.0.zip(r-4.3)
hdxmsqc_1.3.0.tgz(r-4.4-any)hdxmsqc_1.3.0.tgz(r-4.3-any)
hdxmsqc_1.3.0.tar.gz(r-4.5-noble)hdxmsqc_1.3.0.tar.gz(r-4.4-noble)
hdxmsqc_1.3.0.tgz(r-4.4-emscripten)hdxmsqc_1.3.0.tgz(r-4.3-emscripten)
hdxmsqc.pdf |hdxmsqc.html✨
hdxmsqc/json (API)
NEWS

# Install 'hdxmsqc' in R:

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

Bug tracker:https://github.com/ococrook/hdxmsqc/issues

Datasets:

BRD4df - This is data to be included in my package
BRD4df_full - This is data to be included in my package

On BioConductor:hdxmsqc-1.3.0(bioc 3.21)hdxmsqc-1.2.0(bioc 3.20)

qualitycontrol dataimport proteomics massspectrometry metabolomics

4.48 score 2 scripts 159 downloads 23 exports 112 dependencies

Last updated 2 months agofrom:75e2815117. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 29 2024
R-4.5-win	NOTE	Nov 29 2024
R-4.5-linux	NOTE	Nov 29 2024
R-4.4-win	NOTE	Nov 29 2024
R-4.4-mac	NOTE	Nov 29 2024
R-4.3-win	NOTE	Nov 29 2024
R-4.3-mac	NOTE	Nov 29 2024

Exports:chargeCorrelationHdx compatibleUptake computeMassError computeMonotoneStats exchangeableAmides fourierIsotope generateSpectra imTimeOutlier intensityOutliers isMissingAtRandom isotopicDistributionHDXfourier plotImTimeOutlier plotIntensityOutliers plotMassError plotMissing plotMonotoneStat plotrTimeOutliers processHDE qualityControl replicateCorrelation replicateOutlier rTimeOutliers spectraSimilarity

Dependencies:abind AnnotationFilter askpass base64enc BH Biobase BiocBaseUtils BiocGenerics BiocManager BiocParallel BiocStyle bookdown bslib cachem cli clue cluster codetools colorspace cpp11 crayon crosstalk curl data.table DelayedArray digest dplyr evaluate fansi farver fastmap fontawesome formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gtable highr htmltools htmlwidgets httr igraph IRanges isoband jquerylib jsonlite knitr labeling lambda.r later lattice lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise MetaboCoreUtils mgcv mime MsCoreUtils MultiAssayExperiment munsell nlme openssl pillar pkgconfig plotly plyr promises ProtGenerics purrr QFeatures R6 rappdirs RColorBrewer Rcpp reshape2 rlang rmarkdown S4Arrays S4Vectors sass scales snow SparseArray Spectra stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex UCSC.utils utf8 vctrs viridisLite withr xfun XVector yaml zlibbioc

qc-tidying

Oliver M. Crook

Rendered fromqc-streamlined.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2024-06-30
Started: 2024-01-31

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
This is data to be included in my package	BRD4df
This is data to be included in my package	BRD4df_full
Charge states should have correlated incorperation but they need not be exactly the same	chargeCorrelationHdx
Check whether deuterium uptakes are compatible with difference overlapping sequences.	compatibleUptake
Empirical versus theoretical mass errors	computeMassError
Monotonicity based outlier detection.	computeMonotoneStats
Compute exchangeable amides.	exchangeableAmides
fourier transform approach to computing isotopic distribution	fourierIsotope
generate Spectra using a fourier transform	generateSpectra
A package to perfrom quality control for mass-spectrometry based hydrogen deuterium exchange experiment.	hdxmsqc
Ion Mobility time based outlier analysis	imTimeOutlier
Intensity based deviations	intensityOutliers
Missing at random versus missing not at random	isMissingAtRandom
fourier transform approach to computing isotopic distribution	isotopicDistributionHDXfourier
Ion Mobility time based outlier analysis	plotImTimeOutlier
Intensity based deviation plot	plotIntensityOutliers
Mass error plot	plotMassError
missing value plot	plotMissing
Monotonicity based outlier detection, plot.	plotMonotoneStat
Retention time based analysis	plotrTimeOutliers
Function to curate and HDExaminer file so that in contains all the information in a sensible format. This object can then be straightforwardly passed to a object of class 'QFeatures'	processHDE
Quality Control table function. Generate a table that collates quality control metrics	qualityControl
Correlation based checks	replicateCorrelation
Correlation based checks	replicateOutlier
Retention time based analysis	rTimeOutliers
Spectral checking using data from HDsite	spectraSimilarity