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Last data update: 2014.03.03

R: Plot probes

plotProbe

R Documentation

Plot probes

Description

Pairwise plot probes of a probeset.

Usage

plotProbe(affy,probeset,probe=NA,probeXY=NA,scan=TRUE,ind,exmask="none",seqmask="none",names=FALSE)

Arguments

`affy`	An object of class `AffyBatch`.
`probeset`	Probe set name (Affymetrix ID).
`probe`	Number of the main probe.
`probeXY`	If probe is NA the x and y coordinates of the main probe can be given in the format 'x.y'.
`scan`	If scan is 'TRUE', each probewise comparison of the probe against all other probes in this probeset will be performed seperately. If scan is 'FALSE', all plots will be plotted in one layout. The layout has 3 columns. If the number of remaining probes that the probe should be compared with is not a multiple of 3, the number of probes will be reduced to the next lower multiple of 3.
`ind`	Numeric vector, with values 1 and 2, definining group assignement for samples in `affy`.
`exmask`	Optional: an expression mask object for this affy batch. Data frame with probe information, for example first element of the output of function `mask`. Should contain: column 1: probe x-coordinate, column 2:probe y coordinate, column 3: probeset, column 4: quality score: values to based filtering on, probes with values smaller than cutoff are discarded.
`seqmask`	Optional: a sequence mask object for this mask.
`names`	If 'TRUE' , the sample names are plotted to identify each individual.

Details

The function plotProbe plots single probe against all other probes of its probe set. The information from the expression based mask, the sequence based mask and the test for the two plotted probes is shown.

Author(s)

Michael Dannemann

References

Dannemann et al, The effects of probe binding affinity differences on gene expression measurements and how to deal with them. Bioinformatics 2009

Examples

data(exmask)
data(AffyBatch)
## plot for one probe comparisons with other probes of the probeset
## for a random probeset
availableProbesets <- as.character(unique(exmask$probes[,4]))
availableProbesets
## scan the plots
## Not run: plotProbe(affy=newAffyBatch,probeset=availableProbesets[22],probe=5,scan=TRUE,ind=rep(1:2,each=10),exmask=exmask$probes,seqmask=sequenceMask)
## scan with names=TRUE
## Not run: plotProbe(affy=newAffyBatch,probeset=availableProbesets[22],probe=5,scan=TRUE,ind=rep(1:2,each=10),exmask=exmask$probes,seqmask=sequenceMask,names=TRUE)
## plot with given x y information
## Not run: plotProbe(affy=newAffyBatch,probeset=availableProbesets[22],probeXY="313.415",scan=TRUE,ind=rep(1:2,each=10),exmask=exmask$probes,seqmask=sequenceMask,names=TRUE)
## all plots in one layout
plotProbe(affy=newAffyBatch,probeset=availableProbesets[22],probe=5,scan=FALSE,ind=rep(1:2,each=10),exmask=exmask$probes,seqmask=sequenceMask)

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(maskBAD)
Loading required package: gcrma
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, 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

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")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/maskBAD/plotProbe.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotProbe
> ### Title: Plot probes
> ### Aliases: plotProbe
> ### Keywords: internal
> 
> ### ** Examples
> 
> data(exmask)
> data(AffyBatch)
> ## plot for one probe comparisons with other probes of the probeset
> ## for a random probeset
> availableProbesets <- as.character(unique(exmask$probes[,4]))
> availableProbesets
  [1] "1000_at"   "1001_at"   "1002_f_at" "1003_s_at" "1004_at"   "1005_at"  
  [7] "1006_at"   "1007_s_at" "1008_f_at" "1009_at"   "100_g_at"  "1010_at"  
 [13] "1011_s_at" "1012_at"   "1013_at"   "1014_at"   "1015_s_at" "1016_s_at"
 [19] "1017_at"   "1018_at"   "101_at"    "1020_s_at" "1021_at"   "1022_f_at"
 [25] "1023_at"   "1024_at"   "1025_g_at" "1026_s_at" "1027_at"   "1028_at"  
 [31] "1029_s_at" "102_at"    "1030_s_at" "1031_at"   "1038_s_at" "1039_s_at"
 [37] "1052_s_at" "1058_at"   "1059_at"   "1060_g_at" "1064_at"   "1073_at"  
 [43] "1074_at"   "1081_at"   "1091_at"   "1101_at"   "1119_at"   "1122_f_at"
 [49] "1130_at"   "1131_at"   "1134_at"   "113_i_at"  "1147_at"   "1151_at"  
 [55] "1154_at"   "1158_s_at" "1160_at"   "1161_at"   "1166_at"   "1173_g_at"
 [61] "1179_at"   "1180_g_at" "1182_at"   "1184_at"   "1191_s_at" "1192_at"  
 [67] "1195_s_at" "1199_at"   "1201_at"   "1211_s_at" "1213_at"   "1217_g_at"
 [73] "121_at"    "1235_at"   "1238_at"   "1241_at"   "1248_at"   "1250_at"  
 [79] "1251_g_at" "1252_at"   "1253_at"   "1268_at"   "1269_at"   "1270_at"  
 [85] "1287_at"   "1288_s_at" "1295_at"   "1307_at"   "1309_at"   "1310_at"  
 [91] "1311_at"   "1312_at"   "1313_at"   "1314_at"   "1315_at"   "1316_at"  
 [97] "1323_at"   "1336_s_at" "1346_at"   "1355_g_at"
> ## scan the plots
> ## Not run: plotProbe(affy=newAffyBatch,probeset=availableProbesets[22],probe=5,scan=TRUE,ind=rep(1:2,each=10),exmask=exmask$probes,seqmask=sequenceMask)
> ## scan with names=TRUE
> ## Not run: plotProbe(affy=newAffyBatch,probeset=availableProbesets[22],probe=5,scan=TRUE,ind=rep(1:2,each=10),exmask=exmask$probes,seqmask=sequenceMask,names=TRUE)
> ## plot with given x y information
> ## Not run: plotProbe(affy=newAffyBatch,probeset=availableProbesets[22],probeXY="313.415",scan=TRUE,ind=rep(1:2,each=10),exmask=exmask$probes,seqmask=sequenceMask,names=TRUE)
> ## all plots in one layout
> plotProbe(affy=newAffyBatch,probeset=availableProbesets[22],probe=5,scan=FALSE,ind=rep(1:2,each=10),exmask=exmask$probes,seqmask=sequenceMask)
> 
> 
> 
> 
> dev.off()
null device 
          1 
>