Last data update: 2014.03.03

 R: massi_select
massi_selectR Documentation

massi_select

Description

This function selects the y chromosome probe data for each sample.

Usage

massi_select(expression_data, y_probes, threshold = 3)

Arguments

expression_data

The expression.data item contains normalized array expression data for all samples. This can be a data.frame with sample names as columns and probe id's as row names. This argument also allows the specification of an ExpressionSet object.

y_probes

A data.frame of probe id's in one column that match y chromosome genes for the array platform. massiR includes probes for several Illumina and Affymetrix platforms. Details on using these probes are included in the vignette and the y.probes manual.

threshold

The threshold value corresponds to probe variation quantiles. This option allows the selection of the most variable probes. Deciding on a probe threshold value should be informed by viewing the plot generated by the massi_y_plot function. Threshold must be an integer "1", "2", "3", or "4". A threshold of "1" will select all y chromosome probes matching the id's in y.probes, Thresholds of "2", "3" and "4" will select probes with a CV in the top 75%, 50% and 25% respectively. The aim here is to remove probes with little to no variance across the samples. Default = 3.

Value

A data.frame containing the subset of y chromosome probe values for each sample.

Author(s)

Sam Buckberry

See Also

massi_y, massi_cluster, massi_y_plot, massi_dip, massi_cluster_plot

Examples


data(massi.test.dataset, massi.test.probes)

massi_select(expression_data=massi.test.dataset, y_probes=massi.test.probes)

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(massiR)
Loading required package: cluster
Loading required package: gplots

Attaching package: 'gplots'

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

    lowess

Loading required package: diptest
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")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/massiR/massi_select.Rd_%03d_medium.png", width=480, height=480)
> ### Name: massi_select
> ### Title: massi_select
> ### Aliases: massi_select
> 
> ### ** Examples
> 
> 
> data(massi.test.dataset, massi.test.probes)
> 
> massi_select(expression_data=massi.test.dataset, y_probes=massi.test.probes)
                   S1       S2       S3       S4       S5       S6       S7
ILMN_1653471 5.628053 5.572770 5.800105 5.757356 5.709985 5.665758 5.698606
ILMN_1670821 5.746427 5.686032 6.307110 6.179258 6.594808 5.433667 5.572385
ILMN_1685690 5.459125 5.567289 6.919465 6.789817 6.559376 5.461153 5.551516
ILMN_1690753 5.257412 5.416448 5.394499 5.484094 5.226605 5.311065 5.500072
ILMN_1731521 5.264909 5.449214 5.490302 5.236805 5.321966 5.240653 5.293508
ILMN_1735767 5.618107 5.708841 5.639277 5.793536 5.706727 5.600248 5.628924
ILMN_1739587 5.883483 5.764190 6.441775 6.438789 6.707278 5.631027 5.681072
ILMN_1755537 5.882456 5.831844 8.133164 8.052959 8.298985 5.132404 5.262697
ILMN_1756506 5.339323 5.633227 5.494657 5.563024 5.630941 5.476826 5.726721
ILMN_1772163 5.696833 5.680091 5.907170 6.017871 6.465122 5.705901 5.635037
ILMN_1776195 5.415901 5.379810 5.722163 5.962179 5.608771 5.489537 5.711136
ILMN_1790515 5.620987 5.695577 5.631488 5.599657 5.582757 5.590639 5.738041
ILMN_1804958 5.815093 5.654395 5.929610 6.104089 5.868732 5.668124 5.672144
ILMN_1805519 6.894205 7.113050 6.810146 7.235299 6.455811 7.149655 7.146553
                   S8       S9      S10      S11      S12      S13      S14
ILMN_1653471 5.870193 5.773197 5.804669 5.787333 5.623842 5.742208 5.812620
ILMN_1670821 6.297744 5.602025 6.571926 5.514589 6.329377 5.390053 5.622378
ILMN_1685690 6.411688 5.425719 6.510781 5.385685 6.723347 5.792421 5.612097
ILMN_1690753 5.389507 5.451285 5.529005 5.435475 5.475273 5.335215 5.494501
ILMN_1731521 5.258408 5.486080 5.254235 5.298765 5.418769 5.319336 5.277203
ILMN_1735767 5.693445 5.632326 5.673751 5.850663 5.865562 5.784582 5.673009
ILMN_1739587 6.369710 5.717710 6.589587 5.860967 6.550993 5.674658 5.647269
ILMN_1755537 8.775304 5.177616 8.599597 5.228302 8.437863 5.306968 5.249797
ILMN_1756506 5.624751 5.500866 5.668513 5.251253 5.799487 5.535710 5.439861
ILMN_1772163 6.070478 5.621025 6.282586 5.488122 6.370546 5.746861 5.668687
ILMN_1776195 5.523489 5.462315 5.473537 5.415247 5.694085 5.545539 5.278787
ILMN_1790515 5.674314 5.718269 5.732012 5.586881 5.630221 5.653870 5.684392
ILMN_1804958 6.140807 5.683996 6.052908 5.686048 6.090642 5.642415 5.661641
ILMN_1805519 7.142735 6.568693 6.639254 6.663388 6.418179 7.315777 7.277047
                  S15      S16      S17      S18      S19      S20      S21
ILMN_1653471 5.928781 5.717976 5.711266 5.871819 5.752710 5.822771 5.958869
ILMN_1670821 5.466512 6.596842 5.580044 6.457961 5.669013 6.433389 6.225647
ILMN_1685690 5.485553 6.607705 5.570400 6.687437 5.799006 6.790464 6.780622
ILMN_1690753 5.533117 5.369657 5.404446 5.506389 5.709315 5.494542 5.408728
ILMN_1731521 5.267636 5.508156 5.288549 5.327463 5.323285 5.364068 5.436508
ILMN_1735767 5.556526 5.673819 5.734599 5.763708 5.675720 5.861843 5.858787
ILMN_1739587 5.723586 6.339614 5.570079 6.496907 5.528109 6.760365 6.333713
ILMN_1755537 5.265650 8.847392 5.340366 8.042633 5.379298 8.673636 8.653485
ILMN_1756506 5.546874 5.674924 5.519294 5.562167 5.509768 5.756456 5.613633
ILMN_1772163 5.763958 5.947003 5.680497 5.750769 5.797046 6.398919 6.098225
ILMN_1776195 5.491419 5.656449 5.484471 5.540061 5.427713 5.410816 5.512437
ILMN_1790515 5.343025 5.518922 5.581188 5.644267 5.483431 5.564931 5.573750
ILMN_1804958 5.695522 6.092516 5.605797 6.307983 5.634230 5.859951 6.300649
ILMN_1805519 7.712217 7.316044 6.939123 7.263498 6.881021 6.572045 7.543241
                  S22      S23      S24      S25      S26      S27      S28
ILMN_1653471 6.068064 5.849426 5.715791 5.890136 5.536594 5.772410 5.726607
ILMN_1670821 6.274444 6.944503 5.688317 6.989044 6.723135 5.501287 5.502067
ILMN_1685690 6.373808 6.910144 5.441819 6.643899 6.613377 5.492018 5.424666
ILMN_1690753 5.707323 5.457991 5.396899 5.345959 5.423556 5.466961 5.675017
ILMN_1731521 5.367202 5.301038 5.241199 5.462394 5.216115 5.336560 5.366636
ILMN_1735767 5.733000 5.735894 5.674420 5.630351 5.728400 5.754697 5.673956
ILMN_1739587 6.609166 6.751257 5.795653 6.508251 6.666033 5.712277 5.907333
ILMN_1755537 8.838049 8.793543 5.143470 9.058472 8.530085 5.266863 5.450601
ILMN_1756506 5.534098 5.746484 5.531503 5.915858 5.601442 5.513399 5.473804
ILMN_1772163 6.148201 6.248996 5.677314 6.063894 6.213402 5.503867 5.761064
ILMN_1776195 5.791567 5.531014 5.339201 5.679496 5.888384 5.559763 5.537902
ILMN_1790515 5.439380 5.615899 5.556946 5.551015 5.644439 5.578891 5.615743
ILMN_1804958 5.949388 6.183928 5.578889 5.854669 6.001077 5.694995 5.637301
ILMN_1805519 6.780830 7.132044 7.027730 6.876599 6.742097 6.530637 7.161702
                  S29      S30      S31      S32      S33      S34      S35
ILMN_1653471 5.680455 5.630664 5.648595 5.491701 5.537499 5.655961 5.624031
ILMN_1670821 5.899301 5.538895 5.961843 6.303986 5.353780 6.417065 6.320205
ILMN_1685690 6.843484 5.591535 6.732637 6.837242 5.605886 6.710500 6.750518
ILMN_1690753 5.380234 5.564181 5.452494 5.501431 5.623815 5.479485 5.494853
ILMN_1731521 5.395938 5.368628 5.467618 5.384446 5.320448 5.498129 5.560777
ILMN_1735767 5.578839 5.662650 5.585370 5.683611 5.669267 5.745183 5.661070
ILMN_1739587 6.463889 5.778337 6.456179 6.301139 5.761900 6.648721 6.421352
ILMN_1755537 8.794241 5.176548 8.781041 8.258582 5.475359 8.574374 8.582037
ILMN_1756506 5.468684 5.516616 5.583324 5.585944 5.458227 5.395737 5.698882
ILMN_1772163 5.920199 5.745944 5.974846 6.023233 5.870849 6.171110 5.916128
ILMN_1776195 5.634415 5.550777 5.596107 5.589934 5.490452 5.659529 5.585207
ILMN_1790515 5.691583 5.526801 5.592938 5.574725 5.404946 5.410267 5.567677
ILMN_1804958 6.223555 5.660200 6.217654 6.259144 5.533854 6.088622 6.160071
ILMN_1805519 7.210230 6.873060 7.322470 7.375892 6.981010 6.543797 7.637724
                  S36      S37      S38      S39      S40      S41      S42
ILMN_1653471 5.524785 5.939116 6.111545 6.184740 5.808058 5.683384 5.788488
ILMN_1670821 6.084410 5.397038 5.980638 5.313078 5.371299 5.397013 6.339462
ILMN_1685690 6.662736 5.587510 6.539260 5.665840 5.641038 5.701969 6.652704
ILMN_1690753 5.453790 5.421385 5.414385 5.605486 5.606017 5.484590 5.327121
ILMN_1731521 5.409575 5.422856 5.412797 5.277427 5.041803 5.438755 5.480432
ILMN_1735767 5.624663 6.003763 6.324859 6.039925 5.740948 5.828655 5.684155
ILMN_1739587 6.491521 5.757518 6.249917 5.832536 5.604884 5.903338 6.489416
ILMN_1755537 8.655416 5.183962 8.184674 5.269346 5.377922 5.061278 8.807824
ILMN_1756506 5.565541 5.345576 5.519150 5.598726 5.480002 5.500093 5.696756
ILMN_1772163 6.105146 5.762257 5.804803 5.679870 5.731318 5.568025 6.230631
ILMN_1776195 5.403168 5.485847 5.481522 5.376567 5.386894 5.358400 5.668100
ILMN_1790515 5.727132 5.774564 5.567656 5.539495 5.550317 5.671070 5.766226
ILMN_1804958 6.211591 5.727706 6.022989 5.655317 5.690620 5.586535 6.036521
ILMN_1805519 7.407917 6.922843 7.432018 7.272892 7.085333 7.501693 7.364942
                  S43      S44      S45      S46      S47      S48      S49
ILMN_1653471 6.114265 5.784431 5.741222 5.884627 5.913877 5.765437 5.794374
ILMN_1670821 6.428168 5.614434 6.492740 5.596998 5.405996 5.495204 6.192988
ILMN_1685690 6.896639 5.644016 6.877958 5.798212 5.776012 5.733813 6.989054
ILMN_1690753 5.560150 5.541454 5.540053 5.494491 5.449138 5.580865 5.579171
ILMN_1731521 5.449568 5.280573 5.442402 5.372567 5.346547 5.316567 5.400035
ILMN_1735767 5.921353 5.716273 5.806849 5.656297 5.567196 5.633248 5.755380
ILMN_1739587 6.356649 5.813927 6.534293 5.708621 5.694118 5.595416 6.241404
ILMN_1755537 8.393787 5.313137 8.835195 5.346936 5.387107 5.373885 8.883519
ILMN_1756506 5.695021 5.474529 5.794440 5.399928 5.424439 5.433860 5.650155
ILMN_1772163 6.109600 5.616881 6.250544 5.660058 5.584271 5.743265 6.091303
ILMN_1776195 5.526122 5.422505 5.648252 5.298904 5.438012 5.424332 5.712231
ILMN_1790515 5.981298 5.760181 5.623841 5.547076 5.460144 5.475102 5.598523
ILMN_1804958 6.216092 5.678877 5.862310 5.660211 5.571331 5.646604 6.129509
ILMN_1805519 6.648476 6.801565 6.611926 7.020946 7.669491 6.255069 7.519692
                  S50      S51      S52      S53      S54      S55      S56
ILMN_1653471 5.803176 5.600676 5.771490 5.758297 5.987993 5.855520 5.843898
ILMN_1670821 5.873663 6.014352 5.843358 6.064396 5.954104 5.712192 6.154072
ILMN_1685690 6.631753 6.833867 5.441978 7.064672 6.799675 5.437134 6.747914
ILMN_1690753 5.479843 5.519307 5.580461 5.446313 5.415748 5.497194 5.509978
ILMN_1731521 5.565646 5.287877 5.309582 5.314364 5.504465 5.242757 5.228559
ILMN_1735767 5.770530 5.748245 5.698656 5.694867 6.009923 5.902817 5.685734
ILMN_1739587 6.010255 6.525401 5.875317 6.284200 6.315084 5.700359 6.386336
ILMN_1755537 7.835949 8.014464 5.933515 7.802482 7.878513 5.896986 7.975067
ILMN_1756506 5.644476 5.527770 5.542016 5.692759 5.574973 5.508056 5.476436
ILMN_1772163 5.798467 5.950167 5.782320 6.284713 6.171025 5.708467 6.123360
ILMN_1776195 5.456097 5.545294 5.400686 5.697217 5.729715 5.186413 5.626539
ILMN_1790515 5.731955 5.580139 5.619479 5.628839 5.496497 5.499385 5.592681
ILMN_1804958 5.900990 6.029696 5.779041 5.819249 5.981667 5.840429 5.848504
ILMN_1805519 6.958797 7.232548 6.719750 6.721429 7.259358 7.041874 7.123581
                  S57      S58      S59      S60
ILMN_1653471 5.703515 5.931072 5.831610 5.888604
ILMN_1670821 6.459221 5.656904 5.716049 5.786861
ILMN_1685690 6.617757 5.416518 5.539063 5.620546
ILMN_1690753 5.315443 5.690792 5.470337 5.627921
ILMN_1731521 5.329113 5.443520 5.410091 5.330439
ILMN_1735767 5.722868 5.842676 5.521675 5.690073
ILMN_1739587 6.366647 5.944415 5.891824 5.924962
ILMN_1755537 7.713152 5.993211 5.963087 5.903832
ILMN_1756506 5.622309 5.679236 5.596572 5.575405
ILMN_1772163 6.025702 5.916913 5.692122 5.819773
ILMN_1776195 5.754908 5.412054 5.334806 5.422449
ILMN_1790515 5.583579 5.681173 5.465022 5.666485
ILMN_1804958 5.842676 5.943555 5.843501 5.805970
ILMN_1805519 6.770132 7.624166 7.001092 7.141416
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>


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