Find Differentially Expressed Genes

Description

Returns differentially expressed genes between two conditions.

Usage

getDifferentialExpressedGenes(x, groups, g1, g2, theta = 0.5, FDRcutoff = 0.05)

Arguments

Details

Differentially expressed features are selected based on a t-test with the adjusted p-value cutoff specified by FDRcutoff.

The filtering selects only features whose variance is greater than the quantile defined by the probability theta.

Value

Integer vector containing indices of differentially expressed features from x.

Author(s)

Wolfgang Huber, 2013

Examples

data(x)
groups = with(pData(x), list(
  "E3.25"       = which(genotype=="WT" & Embryonic.day=="E3.25"),
  "E3.5 (EPI)"  = which(genotype=="WT" & Embryonic.day=="E3.5" & lineage=="EPI"),
  "E3.5 (PE)"   = which(genotype=="WT" & Embryonic.day=="E3.5" & lineage=="PE")))
  
# get a list of differentially expressed genes along the transition from E3.25 to E3.5
de = union(
  getDifferentialExpressedGenes(x, groups, "E3.25", "E3.5 (EPI)"),
  getDifferentialExpressedGenes(x, groups, "E3.25", "E3.5 (PE)"))
fData(x[de,])$symbol

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(Hiiragi2013)
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")'.

Loading required package: boot
Loading required package: clue
Loading required package: cluster
Loading required package: genefilter
Loading required package: geneplotter
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Attaching package: 'lattice'

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

    melanoma

Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
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Attaching package: 'S4Vectors'

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    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: XML
Loading required package: gplots

Attaching package: 'gplots'

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    space

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    lowess

Loading required package: gtools

Attaching package: 'gtools'

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    inv.logit, logit

Loading required package: KEGGREST
Loading required package: MASS

Attaching package: 'MASS'

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    select

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Loading required package: mouse4302.db
Loading required package: org.Mm.eg.db


Loading required package: RColorBrewer
Loading required package: xtable
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Hiiragi2013/getDifferentialExpressedGenes.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getDifferentialExpressedGenes
> ### Title: Find Differentially Expressed Genes
> ### Aliases: getDifferentialExpressedGenes
> 
> ### ** Examples
> 
> data(x)
> groups = with(pData(x), list(
+   "E3.25"       = which(genotype=="WT" & Embryonic.day=="E3.25"),
+   "E3.5 (EPI)"  = which(genotype=="WT" & Embryonic.day=="E3.5" & lineage=="EPI"),
+   "E3.5 (PE)"   = which(genotype=="WT" & Embryonic.day=="E3.5" & lineage=="PE")))
>   
> # get a list of differentially expressed genes along the transition from E3.25 to E3.5
> de = union(
+   getDifferentialExpressedGenes(x, groups, "E3.25", "E3.5 (EPI)"),
+   getDifferentialExpressedGenes(x, groups, "E3.25", "E3.5 (PE)"))
> fData(x[de,])$symbol
  [1] "Liph"          "Gnpnat1"       "Ifitm3"        "Lifr"         
  [5] "Map1lc3a"      "Atg9a"         "Timd2"         "Socs3"        
  [9] "Psmd6"         "Ivns1abp"      "1435789_x_at"  "Ddx39"        
 [13] "Phgdh"         "Psmb4"         "Rad21"         "Gpd1l"        
 [17] "Mal"           "Bhmt"          "Cox7a2l"       "1420043_s_at" 
 [21] "Myadm"         "Ddx39"         "Phgdh"         "Slc7a3"       
 [25] "Mal"           "Fgd1"          "1450882_s_at"  "9430016H08Rik"
 [29] "Cat"           "Acadl"         "Praf2"         "Trim28"       
 [33] "Pltp"          "Jam2"          "1436032_at"    "Gm11517"      
 [37] "Rpl27a"        "Pygm"          "Metap2"        "1439415_x_at" 
 [41] "Klhdc4"        "Odc1"          "Wwtr1"         "Ephx2"        
 [45] "Nudt4"         "Ubc"           "Timd2"         "Vapa"         
 [49] "Igbp1"         "1441931_x_at"  "E2f5"          "Znhit1"       
 [53] "Gm6787"        "Psat1"         "Prps1"         "Ywhaz"        
 [57] "Tomm20"        "1456471_x_at"  "Lamtor1"       "Morc1"        
 [61] "Fam101b"       "Ppa1"          "Sf3a2"         "Ppp1r14d"     
 [65] "Nedd4"         "1429775_a_at"  "Sord"          "Ndufa4"       
 [69] "Lifr"          "Pth1r"         "Serpinh1"      "1447633_x_at" 
 [73] "Serpinh1"      "Foxq1"         "Lama1"         "Spic"         
 [77] "Tfpi"          "Cpn1"          "Gata4"         "Sparc"        
 [81] "Tfpi"          "Crygd"         "Tfap2c"        "Gm20362"      
 [85] "Ybx3"          "Aldh18a1"      "Gsdmd"         "Tfpi"         
 [89] "B3gnt7"        "Col4a1"        "Bmp6"          "Gdpd5"        
 [93] "Sfn"           "Sparc"         "Spic"          "Pramel6"      
 [97] "Itga5"         "Aldh18a1"      "Timp1"         "1439857_at"   
[101] "1435782_at"    "F2r"           "Dkk1"          "Crip2"        
[105] "Trim43a"       "Egr1"          "Lamc1"         "Pgam2"        
[109] "Trim44"        "Dnmt3l"        "Mpped2"        "Glipr2"       
[113] "Hpcal1"        "Sod2"          "Ckap4"         "Gm11545"      
[117] "Zfp934"        "Aldh18a1"      "Aldh18a1"      "1434584_a_at" 
[121] "Icosl"         "Sox17"         "Dhcr7"         "Ptpn18"       
[125] "Alppl2"        "Pramel6"       "Tcf23"         "Fgfr2"        
[129] "Aqp8"          "Akap13"        "Maged1"        "Stmn3"        
[133] "Ckap4"         "1426260_a_at"  "Ppm1b"         "Flrt3"        
[137] "Rhoa"          "P4ha2"         "Tpd52"         "Ywhaz"        
[141] "Wipi2"         "AI503316"      "Tfap2c"        "Tceb1"        
[145] "Klf2"          "Bhmt2"         "Cox7c"         "Fam189a2"     
[149] "Mdk"           "Whrn"          "Cubn"          "Dnaja1"       
[153] "F2r"           "Cyp2s1"        "9630033F20Rik" "Nanog"        
[157] "Ckap4"         "Sox17"         "Nub1"          "B4galt6"      
[161] "Cubn"          "B4galt6"       "Lamb1"         "Atn1"         
[165] "Tcf7l1"        "1438468_at"    "Actn2"         "Acsl5"        
[169] "Slc46a3"       "Ranbp2"        "Creb3l2"       "Fam189a2"     
[173] "Lrr1"          "Psmc4"         "Lmo2"          "Rnf7"         
[177] "1460590_s_at"  "Nub1"          "Bcl2l14"       "Hexb"         
[181] "Foxq1"         "Tfpi"          "Atg4b"         "Whrn"         
[185] "Sap30l"        "Pemt"          "Rffl"          "Sptbn2"       
[189] "Kcnk6"         "1424365_at"    "Pcdh19"        "B4galt6"      
[193] "Rhpn1"         "Nsmce4a"       "1419987_at"    "Glud1"        
[197] "Lamb1"         "Map2k5"        "Foxh1"         "Reep1"        
[201] "Cox7a2"        "Ppt1"          "Esyt3"         "Rab29"        
[205] "Cited2"        "Gpd1l"         "Havcr1"        "Zfp932"       
[209] "1426414_a_at"  "Zmpste24"      "Mrpl22"        "Slc25a39"     
[213] "Col4a2"        "Atg13"         "Eif3i"         "1438503_x_at" 
[217] "Elp3"          "Glg1"          "Eif3l"        
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>