Package: weitrix 1.19.0

Paul Harrison

weitrix: Tools for matrices with precision weights, test and explore weighted or sparse data

Data type and tools for working with matrices having precision weights and missing data. This package provides a common representation and tools that can be used with many types of high-throughput data. The meaning of the weights is compatible with usage in the base R function "lm" and the package "limma". Calibrate weights to account for known predictors of precision. Find rows with excess variability. Perform differential testing and find rows with the largest confident differences. Find PCA-like components of variation even with many missing values, rotated so that individual components may be meaningfully interpreted. DelayedArray matrices and BiocParallel are supported.

Authors:Paul Harrison [aut, cre]

weitrix_1.19.0.tar.gz
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weitrix.pdf |weitrix.html✨
weitrix/json (API)
NEWS

# Install 'weitrix' in R:
install.packages('weitrix', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • simwei - Simulated weitrix dataset.

On BioConductor:weitrix-1.19.0(bioc 3.21)weitrix-1.18.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

softwaredatarepresentationdimensionreductiongeneexpressiontranscriptomicsrnaseqsinglecellregression

4.70 score 8 scripts 214 downloads 24 exports 81 dependencies

Last updated 4 months agofrom:9762181b24. Checks:3 OK, 5 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 19 2025
R-4.5-winNOTEFeb 19 2025
R-4.5-macNOTEFeb 19 2025
R-4.5-linuxNOTEFeb 19 2025
R-4.4-winNOTEFeb 19 2025
R-4.4-macNOTEFeb 19 2025
R-4.3-winOKFeb 19 2025
R-4.3-macOKFeb 19 2025

Exports:as_weitrixbless_weitrixcomponents_seq_screecomponents_seq_screeplotcounts_proportionscounts_shiftmatrix_longweitrix_calibrateweitrix_calibrate_allweitrix_calibrate_trendweitrix_calplotweitrix_componentsweitrix_components_seqweitrix_confectsweitrix_dispersionsweitrix_elistweitrix_hillweitrix_randomizeweitrix_sd_confectsweitrix_weightsweitrix_weights<-weitrix_xweitrix_x<-well_knotted_spline

Dependencies:abindaskpassassertthatBHBiobaseBiocGenericsBiocParallelCkmeans.1d.dpclicodetoolscolorspacecpp11crayoncurlDelayedArrayDelayedMatrixStatsdplyrfansifarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2glm2gluegtablehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclelimmamagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigplyrpurrrR6rbibutilsRColorBrewerRcppRdpackreshape2RhpcBLASctlrlangS4ArraysS4VectorsscalessnowSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsystibbletidyselecttopconfectsUCSC.utilsutf8vctrsviridisLitewithrXVector

Concepts and practical details

Paul Harrison

Rendered fromV1_overview.Rmdusingknitr::rmarkdownon Feb 19 2025.

Last update: 2020-09-02
Started: 2020-03-15

PAT-Seq poly(A) tail length example

Paul Harrison

Rendered fromV2_tail_length.Rmdusingknitr::rmarkdownon Feb 19 2025.

Last update: 2023-10-08
Started: 2020-03-15

PAT-Seq alternative polyadenylation example

Paul Harrison

Rendered fromV3_shift.Rmdusingknitr::rmarkdownon Feb 19 2025.

Last update: 2023-10-08
Started: 2020-03-15

RNA-Seq expression example

Paul Harrison

Rendered fromV4_airway.Rmdusingknitr::rmarkdownon Feb 19 2025.

Last update: 2021-05-10
Started: 2020-03-15

SLAM-Seq proportion data example

Paul Harrison

Rendered fromV5_slam_seq.Rmdusingknitr::rmarkdownon Feb 19 2025.

Last update: 2023-10-08
Started: 2020-09-04

Readme and manuals

Help Manual

Help pageTopics
Convert data to a weitrixas_weitrix
Bless a SummarizedExperiment as a weitrixbless_weitrix
Proportion more variance explained by adding components one at a timecomponents_seq_scree components_seq_screeplot
Produce a weitrix of proportions within groupscounts_proportions
Produce a weitrix of shift scorescounts_shift
Convert a matrix to long form for ggplottingmatrix_long
Simulated weitrix dataset.simwei
Adjust weights row-wise based on given row dispersionsweitrix_calibrate
Adjust weights element-wise by fitting a trend to squared residualsweitrix_calibrate_all
Adjust weights row-wise by fitting a trend to estimated dispersionsweitrix_calibrate_trend
Weight calibration plots, optionally versus a covariateweitrix_calplot
Principal components of a weitrixweitrix_components weitrix_components_seq
Top confident effects based on one or more contrasts of a linear model for each rowweitrix_confects
Calculate row dispersionsweitrix_dispersions
Convert a weitrix object to a limma EList objectweitrix_elist
Calculate Hill numbers (effective number of observations) for rows or columnsweitrix_hill
Generate a random normally distributed version of a weitrixweitrix_randomize
Find rows with confidently excessive variability in a calibrated weitrixweitrix_sd_confects
Get or set a weitrix object's "weights" matrixweitrix_weights weitrix_weights<-
Get or set a weitrix object's "x" matrixweitrix_x weitrix_x<-
Natural cubic spline with good choice of knotswell_knotted_spline