probeplot: probeplot Plot RPA results and probe-level data for a...

Description Usage Arguments Details Value Author(s) References Examples

Description

probeplot Plot RPA results and probe-level data for a specified probeset.

Usage

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probeplot(dat, highlight.probes = NULL, pcol = "darkgrey", hcol = "red",
  cex.lab = 1.5, cex.axis = 1, cex.main = 1, cex.names = 1, main = "",
  ...)

Arguments

dat

Background-corrected and normalized data: probes x samples.

highlight.probes

Optionally highlight some of the probes (with dashed line)

pcol

Color for probe signal visualization.

hcol

Color for probe highlight

cex.lab

Label size adjustment parameters.

cex.axis

Axis size adjustment parameters.

cex.main

Title size adjustment parameters.

cex.names

Names size adjustment parameters.

main

Title text.

...

Other parameters to pass for plot function.

Details

Plots the preprocessed probe-level observations, estimated probeset-level signal, and probe-specific variances. It is also possible to highlight individual probes and external summary measures.

Value

Used for its side-effects. Returns probes x samples matrix of probe-level data plotted on the image.

Author(s)

Leo Lahti leo.lahti@iki.fi

References

See citation("RPA")

Examples

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Example output

Loading required package: affy
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':

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

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")'.

Loading required package: phyloseq

Attaching package: 'phyloseq'

The following object is masked from 'package:affy':

    sampleNames

The following object is masked from 'package:Biobase':

    sampleNames


RPA Copyright (C) 2008-2016 Leo Lahti.
This program comes with ABSOLUTELY NO WARRANTY.
This is free software, and you are welcome to redistribute it under the FreeBSD open source license.

Warning message:
In read.dcf(con) :
  URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't resolve host name'

RPA documentation built on Nov. 8, 2020, 7:47 p.m.