Classifying the eQTLs

Description

It is customary to distinguish two kinds of eQTLs: 1) cis-eQTLs (where the eQTL is on the same locus as the expressed gene); and 2) trans-eQTLs (where the eQTL is on a locus other than that of the expressed gene). The eqtlClassifier allows us to classify the eQTLs as either cis-eQTL or trans-eQTL according to their position in the genome.

Usage

eqtlClassifier(peak, posSNP, posGENE, max)

Arguments

Value

The output of the eqtlClassifier is a data frame where the first column contains the names of each gene, the second column contains the names of markers and the third column contains the PPA value for each significant eQTL. The fourth column contains the number of the chromosome to which the gene belongs, the fifth column contains the start position of the gene and the sixth column contains the end position of the gene. The seventh column contains the number of the chromosome to which the marker belongs, the eighth column contains position of the marker and the ninth column contains a descriptor of the type of eQTL (either cis or trans). Please note that in order to ascertain that an eQTL is either cis or trans, the positions of the markers and the gene need to the given to the function. If one of the values is missing the type of eQTL will be "NA".

Examples

data(PPA.liver)
cutoff.liver <- calculateThreshold(PPA.liver, 0.2)
eqtl.liver <- eqtlFinder(PPA.liver, cutoff.liver)
data(map.liver)
data(probe.liver)
eqtl.type.liver <- eqtlClassifier(eqtl.liver, map.liver, probe.liver,5000000)

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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
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(iBMQ)
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")'.

Loading required package: ggplot2
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/iBMQ/eqtlClassifier.Rd_%03d_medium.png", width=480, height=480)
> ### Name: eqtlClassifier
> ### Title: Classifying the eQTLs
> ### Aliases: eqtlClassifier
> 
> ### ** Examples
> 
> data(PPA.liver)
> cutoff.liver <- calculateThreshold(PPA.liver, 0.2)
> eqtl.liver <- eqtlFinder(PPA.liver, cutoff.liver)
> data(map.liver)
> data(probe.liver)
> eqtl.type.liver <- eqtlClassifier(eqtl.liver, map.liver, probe.liver,5000000)
gene: X1427932_s_at 	: position is missing
gene: X1428670_at 	: position is missing
gene: X1428832_at 	: position is missing
gene: X1436293_x_at 	: position is missing
gene: X1440799_s_at 	: position is missing
gene: X1443814_x_at 	: position is missing
gene: X1455186_a_at 	: position is missing
gene: X1425823_at 	: position is missing
gene: X1429521_at 	: position is missing
gene: X1438035_at 	: position is missing
gene: X1447096_at 	: position is missing
gene: X1459984_at 	: position is missing
gene: X1457027_at 	: position is missing
gene: X1438055_at 	: position is missing
gene: X1439686_at 	: position is missing
gene: X1442109_at 	: position is missing
gene: X1436767_at 	: position is missing
gene: X1435579_at 	: position is missing
gene: X1436753_at 	: position is missing
gene: X1437158_at 	: position is missing
gene: X1437862_at 	: position is missing
gene: X1438072_at 	: position is missing
gene: X1438359_at 	: position is missing
gene: X1438431_at 	: position is missing
gene: X1438751_at 	: position is missing
gene: X1438936_s_at 	: position is missing
gene: X1441727_s_at 	: position is missing
gene: X1442453_at 	: position is missing
gene: X1443056_at 	: position is missing
gene: X1444746_at 	: position is missing
gene: X1447883_x_at 	: position is missing
gene: X1452893_s_at 	: position is missing
gene: X1456822_at 	: position is missing
gene: X1457324_at 	: position is missing
gene: X1457731_at 	: position is missing
gene: X1459747_at 	: position is missing
gene: X1418817_at 	: position is missing
gene: X1420132_s_at 	: position is missing
gene: X1425020_at 	: position is missing
gene: X1427797_s_at 	: position is missing
gene: X1415716_a_at1 	: position is missing
gene: X1415727_at1 	: position is missing
gene: X1415761_at1 	: position is missing
gene: X1428153_at 	: position is missing
gene: X1428652_at 	: position is missing
gene: X1428851_at 	: position is missing
gene: X1429425_at 	: position is missing
gene: X1429900_at 	: position is missing
gene: X1430288_x_at 	: position is missing
gene: X1431109_at 	: position is missing
gene: X1433781_a_at 	: position is missing
gene: X1433789_at 	: position is missing
gene: X1433895_at 	: position is missing
gene: X1436322_a_at 	: position is missing
gene: X1436499_at 	: position is missing
gene: X1437436_s_at 	: position is missing
gene: X1437749_s_at 	: position is missing
gene: X1437878_s_at 	: position is missing
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gene: X1438561_x_at 	: position is missing
gene: X1438858_x_at 	: position is missing
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gene: X1439813_at 	: position is missing
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gene: X1440624_at 	: position is missing
gene: X1440817_x_at 	: position is missing
gene: X1440890_a_at 	: position is missing
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gene: X1441955_s_at 	: position is missing
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gene: X1446802_at 	: position is missing
gene: X1447676_x_at 	: position is missing
gene: X1447800_x_at 	: position is missing
gene: X1447904_s_at 	: position is missing
gene: X1447936_at 	: position is missing
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gene: X1459976_s_at 	: position is missing
gene: X1460014_at 	: position is missing
gene: X1460559_at 	: position is missing
gene: AFFX.MURINE_b1_at1 	: position is missing
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gene: X1438936_s_at 	: position is missing
gene: X1438937_x_at 	: position is missing
gene: X1442510_at 	: position is missing
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gene: X1447458_at 	: position is missing
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gene: X1438936_s_at 	: position is missing
gene: X1438937_x_at 	: position is missing
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gene: X1424948_x_at 	: position is missing
gene: X1434376_at 	: position is missing
gene: X1435769_at 	: position is missing
gene: X1436779_at 	: position is missing
gene: X1446130_at 	: position is missing
gene: X1446368_at 	: position is missing
gene: X1417714_x_at 	: position is missing
gene: X1427932_s_at 	: position is missing
gene: X1431213_a_at 	: position is missing
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gene: X1415760_s_at1 	: position is missing
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gene: X1441274_at 	: position is missing
gene: X1453485_s_at 	: position is missing
gene: X1449321_x_at 	: position is missing
gene: X1435887_at 	: position is missing
gene: X1416128_at 	: position is missing
gene: X1418816_at 	: position is missing
gene: X1418817_at 	: position is missing
gene: X1423275_at 	: position is missing
gene: X1433903_at 	: position is missing
gene: X1435129_at 	: position is missing
gene: X1448715_x_at 	: position is missing
gene: X1455316_x_at 	: position is missing
gene: X1415676_a_at1 	: position is missing
gene: X1415716_a_at1 	: position is missing
gene: X1420219_at 	: position is missing
gene: X1428352_at 	: position is missing
gene: X1428614_at 	: position is missing
gene: X1428692_at 	: position is missing
gene: X1428821_at 	: position is missing
gene: X1433664_at 	: position is missing
gene: X1433895_at 	: position is missing
gene: X1435217_at 	: position is missing
gene: X1436325_at 	: position is missing
gene: X1436644_x_at 	: position is missing
gene: X1436883_at 	: position is missing
gene: X1437070_at 	: position is missing
gene: X1437158_at 	: position is missing
gene: X1437372_at 	: position is missing
gene: X1438699_at 	: position is missing
gene: X1442311_at 	: position is missing
gene: X1442793_s_at 	: position is missing
gene: X1443814_x_at 	: position is missing
gene: X1444487_at 	: position is missing
gene: X1444746_at 	: position is missing
gene: X1445897_s_at 	: position is missing
gene: X1447676_x_at 	: position is missing
gene: X1447800_x_at 	: position is missing
gene: X1447904_s_at 	: position is missing
gene: X1453300_at 	: position is missing
gene: X1453726_s_at 	: position is missing
gene: X1455102_at 	: position is missing
gene: X1455240_x_at 	: position is missing
gene: X1455383_at 	: position is missing
gene: X1455428_at 	: position is missing
gene: X1455454_at 	: position is missing
gene: X1455951_at 	: position is missing
gene: X1456531_x_at 	: position is missing
gene: X1456587_x_at 	: position is missing
gene: X1457398_at 	: position is missing
gene: X1457664_x_at 	: position is missing
gene: X1457669_x_at 	: position is missing
gene: X1458829_at 	: position is missing
gene: X1458947_at 	: position is missing
gene: X1459765_s_at 	: position is missing
gene: X1460559_at 	: position is missing
gene: X1431213_a_at 	: position is missing
gene: X1455892_x_at 	: position is missing
gene: X1428915_at 	: position is missing
gene: X1433933_s_at 	: position is missing
gene: X1434171_at 	: position is missing
gene: X1437749_s_at 	: position is missing
gene: X1438561_x_at 	: position is missing
gene: X1449626_s_at 	: position is missing
gene: X1455186_a_at 	: position is missing
gene: X1441955_s_at 	: position is missing
gene: X1428936_at 	: position is missing
gene: X1429488_at 	: position is missing
gene: X1433571_at 	: position is missing
gene: X1434070_at 	: position is missing
gene: X1441546_at 	: position is missing
gene: X1442109_at 	: position is missing
gene: X1447776_x_at 	: position is missing
gene: X1459948_at 	: position is missing
gene: X1418817_at 	: position is missing
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gene: X1436767_at 	: position is missing
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gene: X1428436_at 	: position is missing
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gene: X1440890_a_at 	: position is missing
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gene: X1441765_at 	: position is missing
gene: X1441881_x_at 	: position is missing
gene: X1441972_at 	: position is missing
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gene: X1442453_at 	: position is missing
gene: X1442593_at 	: position is missing
gene: X1443056_at 	: position is missing
gene: X1443783_x_at 	: position is missing
gene: X1443830_x_at 	: position is missing
gene: X1443983_at 	: position is missing
gene: X1444487_at 	: position is missing
gene: X1444660_at 	: position is missing
gene: X1444746_at 	: position is missing
gene: X1444980_at 	: position is missing
gene: X1446068_at 	: position is missing
gene: X1446127_at 	: position is missing
gene: X1447227_at 	: position is missing
gene: X1447285_at 	: position is missing
gene: X1447448_s_at 	: position is missing
gene: X1447522_s_at 	: position is missing
gene: X1447927_at 	: position is missing
gene: X1452737_at 	: position is missing
gene: X1452852_at 	: position is missing
gene: X1452867_at 	: position is missing
gene: X1452953_at 	: position is missing
gene: X1453028_at 	: position is missing
gene: X1453032_at 	: position is missing
gene: X1453139_at 	: position is missing
gene: X1453160_at 	: position is missing
gene: X1453588_at 	: position is missing
gene: X1454724_x_at 	: position is missing
gene: X1454739_at 	: position is missing
gene: X1454740_at 	: position is missing
gene: X1454774_at 	: position is missing
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gene: X1455130_at 	: position is missing
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gene: X1455244_at 	: position is missing
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gene: X1456898_at 	: position is missing
gene: X1456918_at 	: position is missing
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gene: X1457264_at 	: position is missing
gene: X1457662_x_at 	: position is missing
gene: X1457731_at 	: position is missing
gene: X1457913_at 	: position is missing
gene: X1458469_at 	: position is missing
gene: X1459141_at 	: position is missing
gene: X1459695_at 	: position is missing
gene: X1460006_at 	: position is missing
gene: X1460063_at 	: position is missing
gene: X1460456_at 	: position is missing
gene: X1460603_at 	: position is missing
gene: X1460606_at 	: position is missing
gene: X1457721_at 	: position is missing
gene: X1428832_at 	: position is missing
gene: X1436070_at 	: position is missing
gene: X1441793_at 	: position is missing
gene: X1443807_x_at 	: position is missing
gene: X1444531_at 	: position is missing
gene: X1446118_at 	: position is missing
gene: X1428982_at 	: position is missing
gene: X1420127_s_at 	: position is missing
gene: X1429337_at 	: position is missing
gene: X1433836_a_at 	: position is missing
gene: X1435769_at 	: position is missing
gene: X1436125_at 	: position is missing
gene: X1436229_at 	: position is missing
gene: X1444706_at 	: position is missing
gene: X1445657_at 	: position is missing
Warning messages:
1: In data.frame(as.numeric(res1), as.numeric(res2), as.numeric(res3),  :
  NAs introduced by coercion
2: In data.frame(as.numeric(res1), as.numeric(res2), as.numeric(res3),  :
  NAs introduced by coercion
3: In data.frame(as.numeric(res1), as.numeric(res2), as.numeric(res3),  :
  NAs introduced by coercion
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>