Last data update: 2014.03.03

 R: Export normalized GRanges object to data frame
GR2norm_dfR Documentation

Export normalized GRanges object to data frame

Description

Function to make data frame out of GRanges output of normalizing functions (dtcr(), slograt(), swinsor(), compdata()) for all or a set of chosen transcripts in the file.

Usage

GR2norm_df(norm_GR, RNAid = "all", norm_methods = "all")

Arguments

norm_GR

GRanges object made by other normalization function (dtcr(), slograt(), swinsor(), compdata()) from which data is to be extracted

RNAid

Transcript identifiers of transcripts that are to be extracted

norm_methods

Names of the columns to be extracted.

Value

Data frame object with columns: RNAid, Pos and desired metadata columns (e.g. nt, dtcr)

Author(s)

Lukasz Jan Kielpinski, Nikos Sidiropoulos

See Also

norm_df2GR, dtcr, swinsor, slograt, compdata

Examples

dummy_euc_GR_treated <- GRanges(seqnames="DummyRNA",
                                IRanges(start=round(runif(100)*100),
                                width=round(runif(100)*100+1)), strand="+",
                                EUC=round(runif(100)*100))
dummy_comp_GR_treated <- comp(dummy_euc_GR_treated)
dummy_swinsor <- swinsor(dummy_comp_GR_treated)
GR2norm_df(dummy_swinsor)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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> library(RNAprobR)
Loading required package: GenomicFeatures
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: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
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: 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/RNAprobR/GR2norm_df.Rd_%03d_medium.png", width=480, height=480)
> ### Name: GR2norm_df
> ### Title: Export normalized GRanges object to data frame
> ### Aliases: GR2norm_df
> 
> ### ** Examples
> 
> dummy_euc_GR_treated <- GRanges(seqnames="DummyRNA",
+                                 IRanges(start=round(runif(100)*100),
+                                 width=round(runif(100)*100+1)), strand="+",
+                                 EUC=round(runif(100)*100))
> dummy_comp_GR_treated <- comp(dummy_euc_GR_treated)
Fasta file not specified.
0 % of EUCs removed due to cutoff
> dummy_swinsor <- swinsor(dummy_comp_GR_treated)
> GR2norm_df(dummy_swinsor)
       RNAid Pos nt    swinsor  swinsor.sd
1   DummyRNA   1  0 0.00000000 0.000000000
2   DummyRNA   2  0 0.00000000 0.000000000
3   DummyRNA   3  0 0.44247788 0.000000000
4   DummyRNA   4  0 0.00000000 0.000000000
5   DummyRNA   5  0 0.05309735 0.000000000
6   DummyRNA   6  0 0.48377581 0.000000000
7   DummyRNA   7  0 0.11799410 0.000000000
8   DummyRNA   8  0 0.57817109 0.000000000
9   DummyRNA   9  0 0.46607670 0.000000000
10  DummyRNA  10  0 1.00000000 0.000000000
11  DummyRNA  11  0 0.56182777 0.025133776
12  DummyRNA  12  0 0.00000000 0.000000000
13  DummyRNA  13  0 1.00000000 0.000000000
14  DummyRNA  14  0 0.00000000 0.000000000
15  DummyRNA  15  0 0.00000000 0.000000000
16  DummyRNA  16  0 0.16309777 0.025311252
17  DummyRNA  17  0 0.25210282 0.041349174
18  DummyRNA  18  0 0.00000000 0.000000000
19  DummyRNA  19  0 0.72766998 0.120039632
20  DummyRNA  20  0 0.00000000 0.000000000
21  DummyRNA  21  0 0.00000000 0.000000000
22  DummyRNA  22  0 0.30008944 0.047753707
23  DummyRNA  23  0 0.00000000 0.000000000
24  DummyRNA  24  0 0.00000000 0.000000000
25  DummyRNA  25  0 0.00000000 0.000000000
26  DummyRNA  26  0 0.00000000 0.000000000
27  DummyRNA  27  0 0.26778502 0.041154128
28  DummyRNA  28  0 0.03905737 0.005955757
29  DummyRNA  29  0 0.00000000 0.000000000
30  DummyRNA  30  0 0.17469583 0.026216637
31  DummyRNA  31  0 0.00000000 0.000000000
32  DummyRNA  32  0 0.37326708 0.055115223
33  DummyRNA  33  0 0.00000000 0.000000000
34  DummyRNA  34  0 0.19215044 0.027914695
35  DummyRNA  35  0 0.10864663 0.015656313
36  DummyRNA  36  0 0.54848225 0.078403014
37  DummyRNA  37  0 0.35644682 0.050545360
38  DummyRNA  38  0 0.98464564 0.009134257
39  DummyRNA  39  0 0.43891072 0.060969186
40  DummyRNA  40  0 0.16558047 0.022718828
41  DummyRNA  41  0 0.36340802 0.049265371
42  DummyRNA  42  0 0.00000000 0.000000000
43  DummyRNA  43  0 0.68999154 0.091388637
44  DummyRNA  44  0 1.00000000 0.000000000
45  DummyRNA  45  0 0.41881905 0.057904142
46  DummyRNA  46  0 0.00000000 0.000000000
47  DummyRNA  47  0 0.22215912 0.033193842
48  DummyRNA  48  0 0.32883376 0.050550444
49  DummyRNA  49  0 0.01985267 0.003124668
50  DummyRNA  50  0 0.38609630 0.061976452
51  DummyRNA  51  0 0.00000000 0.000000000
52  DummyRNA  52  0 0.00000000 0.000000000
53  DummyRNA  53  0 0.10148904 0.016992860
54  DummyRNA  54  0 0.00000000 0.000000000
55  DummyRNA  55  0 0.00000000 0.000000000
56  DummyRNA  56  0 0.56967502 0.097827610
57  DummyRNA  57  0 0.61355264 0.105983542
58  DummyRNA  58  0 0.40154087 0.069700457
59  DummyRNA  59  0 0.26415363 0.046036677
60  DummyRNA  60  0 0.00000000 0.000000000
61  DummyRNA  61  0 0.39229450 0.068768438
62  DummyRNA  62  0 0.68199737 0.119790211
63  DummyRNA  63  0 0.00000000 0.000000000
64  DummyRNA  64  0 0.47434776 0.083521769
65  DummyRNA  65  0 1.00000000 0.000000000
66  DummyRNA  66  0 0.00000000 0.000000000
67  DummyRNA  67  0 0.25837390 0.046968184
68  DummyRNA  68  0 0.64911517 0.119510466
69  DummyRNA  69  0 0.10870079 0.020237433
70  DummyRNA  70  0 0.47320525 0.088963547
71  DummyRNA  71  0 0.35928830 0.067917044
72  DummyRNA  72  0 0.33231365 0.063056596
73  DummyRNA  73  0 0.56521818 0.107488887
74  DummyRNA  74  0 0.88938077 0.115423733
75  DummyRNA  75  0 0.00000000 0.000000000
76  DummyRNA  76  0 0.01520425 0.002906983
77  DummyRNA  77  0 0.00000000 0.000000000
78  DummyRNA  78  0 0.30087873 0.057423292
79  DummyRNA  79  0 0.37301738 0.070967393
80  DummyRNA  80  0 0.77492761 0.146756221
81  DummyRNA  81  0 0.67013216 0.126148972
82  DummyRNA  82  0 0.59454137 0.112319852
83  DummyRNA  83  0 0.71734760 0.135873928
84  DummyRNA  84  0 0.56096876 0.106433277
85  DummyRNA  85  0 0.82437454 0.154529959
86  DummyRNA  86  0 0.08065000 0.015684950
87  DummyRNA  87  0 0.37244260 0.073593146
88  DummyRNA  88  0 0.84064968 0.156033224
89  DummyRNA  89  0 1.00000000 0.000000000
90  DummyRNA  90  0 0.00000000 0.000000000
91  DummyRNA  91  0 1.00000000 0.000000000
92  DummyRNA  92  0 0.72910154 0.153629576
93  DummyRNA  93  0 0.00000000 0.000000000
94  DummyRNA  94  0 0.50854872 0.154964851
95  DummyRNA  95  0 0.83441273 0.155682725
96  DummyRNA  96  0 0.63387248 0.154188522
97  DummyRNA  97  0 0.00000000 0.000000000
98  DummyRNA  98  0 0.00000000 0.000000000
99  DummyRNA  99  0 0.05687842 0.168345998
100 DummyRNA 100  0 0.00000000 0.000000000
101 DummyRNA 101  0 0.00000000 0.000000000
102 DummyRNA 102  0 0.00000000 0.000000000
103 DummyRNA 103  0 0.00000000 0.000000000
104 DummyRNA 104  0 0.00000000 0.000000000
105 DummyRNA 105  0 0.00000000 0.000000000
106 DummyRNA 106  0 0.00000000 0.000000000
107 DummyRNA 107  0 0.00000000 0.000000000
108 DummyRNA 108  0 0.00000000 0.000000000
109 DummyRNA 109  0 0.00000000 0.000000000
110 DummyRNA 110  0 0.00000000 0.000000000
111 DummyRNA 111  0 0.00000000 0.000000000
112 DummyRNA 112  0 0.00000000 0.000000000
113 DummyRNA 113  0 0.00000000 0.000000000
114 DummyRNA 114  0 0.00000000 0.000000000
115 DummyRNA 115  0 0.00000000 0.000000000
116 DummyRNA 116  0 0.00000000 0.000000000
117 DummyRNA 117  0 0.00000000 0.000000000
118 DummyRNA 118  0 0.00000000 0.000000000
119 DummyRNA 119  0 0.00000000 0.000000000
120 DummyRNA 120  0 0.00000000 0.000000000
121 DummyRNA 121  0 0.00000000 0.000000000
122 DummyRNA 122  0 0.00000000 0.000000000
123 DummyRNA 123  0 0.00000000 0.000000000
124 DummyRNA 124  0 0.00000000 0.000000000
125 DummyRNA 125  0 0.00000000 0.000000000
126 DummyRNA 126  0 0.00000000 0.000000000
127 DummyRNA 127  0 0.00000000 0.000000000
128 DummyRNA 128  0 0.00000000 0.000000000
129 DummyRNA 129  0 0.00000000 0.000000000
130 DummyRNA 130  0 0.00000000 0.000000000
131 DummyRNA 131  0 0.00000000 0.000000000
132 DummyRNA 132  0 0.00000000 0.000000000
133 DummyRNA 133  0 0.00000000 0.000000000
134 DummyRNA 134  0 0.00000000 0.000000000
135 DummyRNA 135  0 0.00000000 0.000000000
136 DummyRNA 136  0 0.00000000 0.000000000
137 DummyRNA 137  0 0.00000000 0.000000000
138 DummyRNA 138  0 0.00000000 0.000000000
139 DummyRNA 139  0 0.00000000 0.000000000
140 DummyRNA 140  0 0.00000000 0.000000000
141 DummyRNA 141  0 0.00000000 0.000000000
142 DummyRNA 142  0 0.00000000 0.000000000
143 DummyRNA 143  0 0.00000000 0.000000000
144 DummyRNA 144  0 0.00000000 0.000000000
145 DummyRNA 145  0 0.00000000 0.000000000
146 DummyRNA 146  0 0.00000000 0.000000000
147 DummyRNA 147  0 0.00000000 0.000000000
148 DummyRNA 148  0 0.00000000 0.000000000
149 DummyRNA 149  0 0.00000000 0.000000000
150 DummyRNA 150  0 0.00000000 0.000000000
151 DummyRNA 151  0 0.00000000 0.000000000
152 DummyRNA 152  0 0.00000000 0.000000000
153 DummyRNA 153  0 0.00000000 0.000000000
154 DummyRNA 154  0 0.00000000 0.000000000
155 DummyRNA 155  0 0.00000000 0.000000000
156 DummyRNA 156  0 0.00000000 0.000000000
157 DummyRNA 157  0 0.00000000 0.000000000
158 DummyRNA 158  0 0.00000000 0.000000000
159 DummyRNA 159  0 0.00000000 0.000000000
160 DummyRNA 160  0 0.00000000 0.000000000
161 DummyRNA 161  0 0.00000000 0.000000000
162 DummyRNA 162  0 0.00000000 0.000000000
163 DummyRNA 163  0 0.00000000 0.000000000
164 DummyRNA 164  0 0.00000000          NA
165 DummyRNA 165  0         NA          NA
166 DummyRNA 166  0         NA          NA
167 DummyRNA 167  0         NA          NA
168 DummyRNA 168  0         NA          NA
169 DummyRNA 169  0         NA          NA
170 DummyRNA 170  0         NA          NA
171 DummyRNA 171  0         NA          NA
172 DummyRNA 172  0         NA          NA
173 DummyRNA 173  0         NA          NA
174 DummyRNA 174  0         NA          NA
175 DummyRNA 175  0         NA          NA
176 DummyRNA 176  0         NA          NA
177 DummyRNA 177  0         NA          NA
178 DummyRNA 178  0         NA          NA
179 DummyRNA 179  0         NA          NA
180 DummyRNA 180  0         NA          NA
181 DummyRNA 181  0         NA          NA
182 DummyRNA 182  0         NA          NA
183 DummyRNA 183  0         NA          NA
184 DummyRNA 184  0         NA          NA
185 DummyRNA 185  0         NA          NA
186 DummyRNA 186  0         NA          NA
187 DummyRNA 187  0         NA          NA
188 DummyRNA 188  0         NA          NA
189 DummyRNA 189  0         NA          NA
190 DummyRNA 190  0         NA          NA
191 DummyRNA 191  0         NA          NA
192 DummyRNA 192  0         NA          NA
193 DummyRNA 193  0         NA          NA
194 DummyRNA 194  0         NA          NA
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>


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