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Last data update: 2014.03.03

R: Function to calculate chemical genetic interactions

getInteractions

R Documentation

Function to calculate chemical genetic interactions

Description

To detect chemcial genetic interactions, the data of each feature is modeled using a multiplicative model and robust L1 regression to estimate the effects of the cell line and drug treatment using the medpolish function. In this iterative approach row and column median values are subtracted alternately until the proportional change of the absolute residuals falls below a defined threshold. The final row and column values describe the drug and cell line effect respectively. The residuals represent the interaction terms. This process is done for each replicate and each feature individually. To detect significant interactions the values of replicates are used to perform a moderated t-test against the null hypothesis t = 0, using the implementation in the Bioconductor package limma. p-values are adjusted for multiple testing by controlling for the false discovery rate using the method of Benjamini & Hochberg.

Usage

getInteractions(d, ftrs = NULL, samplesOnly = FALSE, scaleByLine = FALSE,
  ...)

Arguments

`d`	`list` containing a `array` with four dimensions of features `D`, a `list` with annotation. The annotation `list` needs to contain a character `vector` `ftr` with the feature names and a character `vector` `drug$Content` defining whether the data comes from "sample" or "other" wells.
`ftrs`	Parameter to select certain features for the caluclation of chemical genetic interactions.
`samplesOnly`	If set to `TRUE` only values of "sample" wells will be used for the calculation of chemical genetic interactions.
`scaleByLine`	If set to `TRUE` the interaction terms for each cell line will be scaled by the median absolute deviation of interaction terms for the individual cell line and replicate.
`...`	Additional parameters passed to `medpolish`

Value

A list with the annotation anno, raw data of the selected features D, the chemical genetic interaction results res, the estimated drug and cell line effect effect and calculated p-values and multiple testing adjusted p-values.

Author(s)

Felix A. Klein, felix.klein@embl.de

Examples

data(interactions)
x <- getInteractions(interactions)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(PGPC)
Loading required package: EBImage
Loading required package: imageHTS
Loading required package: cellHTS2
Loading required package: RColorBrewer
Loading required package: Biobase
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, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, 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, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

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:EBImage':

    channel

Loading required package: genefilter
Loading required package: splots
Loading required package: vsn
Loading required package: hwriter
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: grid
Loading required package: SearchTrees
Loading required package: limma

Attaching package: 'limma'

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

    plotMA

Loading required package: gplots

Attaching package: 'gplots'

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

    lowess

Loading required package: ggplot2

Attaching package: 'ggplot2'

The following object is masked from 'package:cellHTS2':

    annotate

Loading required package: geneplotter
Loading required package: lattice
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    space

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums


Attaching package: 'IRanges'

The following objects are masked from 'package:EBImage':

    resize, tile

Loading required package: XML
Loading required package: ChemmineR

Attaching package: 'ChemmineR'

The following object is masked from 'package:S4Vectors':

    fold

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

    makeUnique

Loading required package: reshape2
Loading required package: plyr

Attaching package: 'plyr'

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

    desc

The following object is masked from 'package:S4Vectors':

    rename

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/PGPC/getInteractions.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getInteractions
> ### Title: Function to calculate chemical genetic interactions
> ### Aliases: getInteractions
> 
> ### ** Examples
> 
> data(interactions)
> x <- getInteractions(interactions)
n :
1: 753.4947
Final: 746.3395
1: 763.7207
Final: 759.436
OK
cseg.act.m.majoraxis.mean :
1: 296.4455
2: 265.2288
Final: 265.1659
1: 296.6415
2: 264.2398
Final: 264.0885
OK
cseg.act.h.cor.s1.mean :
1: 169.3524
2: 162.3747
Final: 162.33
1: 184.2711
2: 176.4016
Final: 176.3536
OK
nseg.0.m.majoraxis.mean :
1: 154.7573
2: 144.5022
Final: 144.4258
1: 156.3483
2: 141.5815
Final: 141.5132
OK
cseg.dnaact.m.eccentricity.sd :
1: 189.4188
2: 178.8628
Final: 178.7885
1: 195.1087
2: 185.5703
Final: 185.5071
OK
cseg.act.h.f12.s2.sd :
1: 619.5657
2: 586.1412
Final: 585.6857
1: 606.0347
2: 574.5846
Final: 574.1621
OK
nseg.dna.h.var.s2.mean :
1: 1495.098
2: 1380.598
Final: 1379.532
1: 1422.128
2: 1321.2
Final: 1320.531
OK
nseg.0.m.eccentricity.mean :
1: 153.705
2: 141.9392
Final: 141.8788
1: 147.6194
2: 136.3516
Final: 136.2635
OK
cseg.0.s.radius.min.qt.0.05 :
1: 980.6066
2: 926.3809
Final: 926.0206
1: 955.4517
2: 902.047
Final: 901.5334
OK
cseg.dnaact.b.mean.qt.0.05 :
1: 2078.829
2: 1854.991
Final: 1854.231
1: 2107.712
2: 1914.145
Final: 1913.606
OK
cseg.act.m.eccentricity.mean :
1: 95.67934
2: 91.1919
Final: 91.13504
1: 86.32976
2: 81.03071
Final: 81.00283
OK
nseg.dna.m.eccentricity.sd :
1: 199.5663
2: 182.3183
Final: 182.2087
1: 191.7516
2: 178.8224
Final: 178.7197
OK
nseg.dna.h.idm.s1.sd :
1: 357.8356
2: 342.754
Final: 342.5477
1: 357.1522
2: 339.67
Final: 339.5059
OK
cseg.dnaact.h.f13.s1.mean :
1: 197.0226
2: 171.6291
Final: 171.4837
1: 227.4053
2: 192.8771
Final: 192.6918
OK
cseg.act.h.asm.s2.mean :
1: 2008.03
2: 1836.704
Final: 1836.008
1: 2030.559
2: 1847.379
Final: 1846.707
OK
cseg.dnaact.h.den.s2.sd :
1: 499.1948
2: 434.7513
Final: 434.5747
1: 512.0984
2: 462.948
Final: 462.7504
OK
nseg.dna.h.cor.s2.sd :
1: 412.4627
2: 378.7482
Final: 378.3287
1: 386.6022
2: 359.8544
Final: 359.5098
OK
cseg.dnaact.b.mad.mean :
1: 1852.733
2: 1594.065
Final: 1592.911
1: 1790.114
2: 1584.728
Final: 1584.147
OK
cseg.act.h.idm.s2.sd :
1: 580.9851
2: 557.3896
Final: 557.0226
1: 582.3771
2: 547.5154
Final: 547.3178
OK
nseg.0.s.radius.max.qt.0.05 :
1: 182.4144
2: 165.5688
Final: 165.471
1: 182.1041
2: 167.2589
Final: 167.1733
OK
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>