h5mat: create a file connection to HDF5 matrix

In BiocSklearn: interface to python sklearn via Rstudio reticulate

Description

create a file connection to HDF5 matrix

Usage

h5mat(infile, mode = "r", ...)

Arguments

infile	a pathname to an HDF5 file
mode	character(1) defaults to "r", see py_help for h5py.File
...	unused

Value

instance of (S3) h5py._hl.files.File

Note

The result of this function must be used with basiliskRun with the env argument set to bsklenv, or there is a risk of inconsistent python modules being invoked. This should only be used with the persistent environment discipline of basilisk.

Examples

if (interactive()) {   # not clear why
fn = system.file("ban_6_17/assays.h5", package="BiocSklearn")
proc = basilisk::basiliskStart(BiocSklearn:::bsklenv)
basilisk::basiliskRun(proc, function(infile, mode="r") {
 h5py = reticulate::import("h5py") 
 hh = h5py$File( infile, mode=mode )
 cat("File reference:\n ")
 print(hh)
 cat("File attributes in python:\n ")
 print(head(names(hh)))
 cat("File keys in python:\n ")
 print(hh$keys())
 cat("HDF5 dataset in python:\n ")
 print(hh['assay001'])
}, infile=fn, mode="r")
basilisk::basiliskStop(proc)
}

Example output

Loading required package: reticulate
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: ‘MatrixGenerics’

The following objects are masked from ‘package:matrixStats’:

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: ‘Biobase’

The following object is masked from ‘package:MatrixGenerics’:

    rowMedians

The following objects are masked from ‘package:matrixStats’:

    anyMissing, rowMedians

Loading required package: knitr

BiocSklearn documentation built on Nov. 8, 2020, 7:52 p.m.