BIOMfrom: Convert BIOM data from formal to basic type (export)
In BIOM.utils: Utilities for the BIOM (Biological Observation Matrix) Format
Description
Usage
Arguments
Details
Value
Author(s)
References
See Also
Examples
Description
Convert an object of class biom into a basic type: matrix, list, or character.
Usage
1
2
3
4
5
6
7
8
Arguments
x
an object (biom)
expand
if sparse, force return of not sparse matrix? (logical)
...
unused
file
filename for writing object
Details
BIOM (Biological Observation Matrix) is a simple prescription
for storing an annotated table of data.
It may be described as a format, standard, or data structure.
The JSON (JavaScript Object Notation) standard
for expressing general data objects as text
is employed to define BIOM.
Therefore the native form of BIOM data is structured text,
conforming to the JSON specification in general
and the BIOM specification in particular.
Familiarity with BIOM is assumed here.
The S3 class biom and its methods facilitate analyses
by expressing BIOM data as objects in the R environment.
Each function above transforms an object that is
already of class biom into a basic R type.
as.matrix() returns the BIOM data table as a matrix.
If the object is "dense", then dimnames() of the result
are equal to the BIOM row and column ids.
Otherwise, the three-column sparse representation matrix is returned,
with ids given by attached attributes "rownames" and "colnames".
However, using expand=TRUE expands a sparse representation.
(Setting expand=FALSE has no effect when the object is "dense".)
Also, see below for an example using class "sparseMatrix"
from the R package Matrix.
as.character() returns BIOM properly speaking, that is,
data and annotations written in JSON text conforming to the BIOM specification.
That text is written to file, if provided.
See below for an example of saving the data table, only, in CSV or TSV format.
Of course, it is possible to bring biom objects
in and out of the session with save() and load().
as.list() returns a list corresponding closely
element-by-element to BIOM. The differences are:
list element data is a matrix not list;
elements rows and columns hold metadata only,
and so do not include ids; instead, additional elements
row.ids and column.ids are present;
and format_url is missing.
Value
For as.matrix() and as.list(), as described.
For as.character(), a single string of JSON text,
or simply file if it is not NULL.
Except that last case, these functions return invisibly.
Author(s)
Daniel T. Braithwaite
References
See Also
Examples
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
tt <- tempfile()
xx <- biom (li3)
yy <- biom (smat, sparse=TRUE, quiet=TRUE)
## extract objects of basic types:
print (as.matrix (xx))
head (as.matrix (yy, expand=TRUE))
as.character (xx)
as.character (xx, file=tt)
str (as.list (xx))
## export to a CSV file:
write.table (as.matrix (xx), file=tt, sep=",")
## Not run:
## a classed sparse matrix (for computation or what have you):
zz <- as.matrix (yy)
zz[,1:2] <- 1 + zz[,1:2]
Matrix::sparseMatrix (i=zz[,1], j=zz[,2], x=zz[,3])
## End(Not run)
unlink(tt)
Example output
BIOM.utils (0.9 dbcb27)
AAA BBB CCC DDD EEE
aaa 101 121 141 161 181
bbb 102 122 142 162 182
ccc 103 123 143 163 183
ddd 104 124 144 164 184
eee 105 125 145 165 185
fff 106 126 146 166 186
ggg 107 127 147 167 187
hhh 108 128 148 168 188
iii 109 129 149 169 189
jjj 110 130 150 170 190
kkk 111 131 151 171 191
lll 112 132 152 172 192
mmm 113 133 153 173 193
nnn 114 134 154 174 194
ooo 115 135 155 175 195
ppp 116 136 156 176 196
qqq 117 137 157 177 197
rrr 118 138 158 178 198
sss 119 139 159 179 199
ttt 120 140 160 180 200
column1 column2 column3 column4
row1 63 140 27 11
row2 11 37 0 75
row3 160 1025 151 2172
row4 0 0 4 0
row5 0 67 6 0
row6 0 38 13 0
[1] "{\n \"id\": \"\",\n\"format\": \"Biological Observation Matrix 1.0\",\n\"type\": \"OTU table\",\n\"generated_by\": \"BIOM.utils (0.9)\",\n\"date\": \"2017-12-14 17:01:08\",\n\"rows\": [\n {\n \"id\": \"aaa\",\n\"metadata\": \"metadata of aaa\" \n},\n{\n \"id\": \"bbb\",\n\"metadata\": \"metadata of bbb\" \n},\n{\n \"id\": \"ccc\",\n\"metadata\": \"metadata of ccc\" \n},\n{\n \"id\": \"ddd\",\n\"metadata\": \"metadata of ddd\" \n},\n{\n \"id\": \"eee\",\n\"metadata\": \"metadata of eee\" \n},\n{\n \"id\": \"fff\",\n\"metadata\": \"metadata of fff\" \n},\n{\n \"id\": \"ggg\",\n\"metadata\": \"metadata of ggg\" \n},\n{\n \"id\": \"hhh\",\n\"metadata\": \"metadata of hhh\" \n},\n{\n \"id\": \"iii\",\n\"metadata\": \"metadata of iii\" \n},\n{\n \"id\": \"jjj\",\n\"metadata\": \"metadata of jjj\" \n},\n{\n \"id\": \"kkk\",\n\"metadata\": \"metadata of kkk\" \n},\n{\n \"id\": \"lll\",\n\"metadata\": \"metadata of lll\" \n},\n{\n \"id\": \"mmm\",\n\"metadata\": \"metadata of mmm\" \n},\n{\n \"id\": \"nnn\",\n\"metadata\": \"metadata of nnn\" \n},\n{\n \"id\": \"ooo\",\n\"metadata\": \"metadata of ooo\" \n},\n{\n \"id\": \"ppp\",\n\"metadata\": \"metadata of ppp\" \n},\n{\n \"id\": \"qqq\",\n\"metadata\": \"metadata of qqq\" \n},\n{\n \"id\": \"rrr\",\n\"metadata\": \"metadata of rrr\" \n},\n{\n \"id\": \"sss\",\n\"metadata\": \"metadata of sss\" \n},\n{\n \"id\": \"ttt\",\n\"metadata\": \"metadata of ttt\" \n} \n],\n\"columns\": [\n {\n \"id\": \"AAA\",\n\"metadata\": \"metadata of AAA\" \n},\n{\n \"id\": \"BBB\",\n\"metadata\": \"metadata of BBB\" \n},\n{\n \"id\": \"CCC\",\n\"metadata\": \"metadata of CCC\" \n},\n{\n \"id\": \"DDD\",\n\"metadata\": \"metadata of DDD\" \n},\n{\n \"id\": \"EEE\",\n\"metadata\": \"metadata of EEE\" \n} \n],\n\"matrix_type\": \"dense\",\n\"matrix_element_type\": \"int\",\n\"shape\": [ 20, 5 ],\n\"data\": [\n [ 101, 121, 141, 161, 181 ],\n[ 102, 122, 142, 162, 182 ],\n[ 103, 123, 143, 163, 183 ],\n[ 104, 124, 144, 164, 184 ],\n[ 105, 125, 145, 165, 185 ],\n[ 106, 126, 146, 166, 186 ],\n[ 107, 127, 147, 167, 187 ],\n[ 108, 128, 148, 168, 188 ],\n[ 109, 129, 149, 169, 189 ],\n[ 110, 130, 150, 170, 190 ],\n[ 111, 131, 151, 171, 191 ],\n[ 112, 132, 152, 172, 192 ],\n[ 113, 133, 153, 173, 193 ],\n[ 114, 134, 154, 174, 194 ],\n[ 115, 135, 155, 175, 195 ],\n[ 116, 136, 156, 176, 196 ],\n[ 117, 137, 157, 177, 197 ],\n[ 118, 138, 158, 178, 198 ],\n[ 119, 139, 159, 179, 199 ],\n[ 120, 140, 160, 180, 200 ] \n],\n\"format_url\": {\n \"Biological Observation Matrix 1.0\": \"http://biom-format.org/documentation/format_versions/biom-1.0.html\" \n} \n}"
[1] "/work/tmp/tmp/RtmpCft7t2/filee0220dec3d4"
List of 14
$ id : chr ""
$ format : chr "Biological Observation Matrix 1.0"
$ type : chr "OTU table"
$ generated_by : chr "BIOM.utils (0.9)"
$ date : chr "2017-12-14 17:01:08"
$ rows :List of 20
..$ : chr "metadata of aaa"
..$ : chr "metadata of bbb"
..$ : chr "metadata of ccc"
..$ : chr "metadata of ddd"
..$ : chr "metadata of eee"
..$ : chr "metadata of fff"
..$ : chr "metadata of ggg"
..$ : chr "metadata of hhh"
..$ : chr "metadata of iii"
..$ : chr "metadata of jjj"
..$ : chr "metadata of kkk"
..$ : chr "metadata of lll"
..$ : chr "metadata of mmm"
..$ : chr "metadata of nnn"
..$ : chr "metadata of ooo"
..$ : chr "metadata of ppp"
..$ : chr "metadata of qqq"
..$ : chr "metadata of rrr"
..$ : chr "metadata of sss"
..$ : chr "metadata of ttt"
$ columns :List of 5
..$ : chr "metadata of AAA"
..$ : chr "metadata of BBB"
..$ : chr "metadata of CCC"
..$ : chr "metadata of DDD"
..$ : chr "metadata of EEE"
$ row.ids : chr [1:20] "aaa" "bbb" "ccc" "ddd" ...
$ column.ids : chr [1:5] "AAA" "BBB" "CCC" "DDD" ...
$ matrix_type : chr "dense"
$ matrix_element_type: chr "int"
$ shape : int [1:2] 20 5
$ data : int [1:20, 1:5] 101 102 103 104 105 106 107 108 109 110 ...
..- attr(*, "dimnames")=List of 2
.. ..$ : chr [1:20] "aaa" "bbb" "ccc" "ddd" ...
.. ..$ : chr [1:5] "AAA" "BBB" "CCC" "DDD" ...
$ comment : NULL
266 x 4 sparse Matrix of class "dgCMatrix"
[1,] 63 140 27 11
[2,] 11 37 . 75
[3,] 160 1025 151 2172
[4,] . . 4 .
[5,] . 67 6 .
[6,] . 38 13 .
[7,] 158 26 55 113
[8,] 15561 3511 4139 14627
[9,] 260 631 247 694
[10,] 109 401 124 95
[11,] 411 880 174 144
[12,] 37 255 28 5
[13,] 31 111 18 168
[14,] 122 469 71 32
[15,] . . 12 1
[16,] . 3 . .
[17,] . 2 2 .
[18,] 7 127 24 153
[19,] . 2 1 5
[20,] 4 8 7 .
[21,] 764 3647 909 3559
[22,] 2256 11759 3915 27659
[23,] 2 20 . 10
[24,] . 11 7 .
[25,] . 51 3 .
[26,] 886 119 230 755
[27,] 856 443 402 7924
[28,] 8 52 15 11
[29,] 122 . . .
[30,] 30 236 48 295
[31,] 61 236 101 47
[32,] . 15 . .
[33,] 496 58 209 268
[34,] 59 106 34 53
[35,] 1696 4431 881 195
[36,] 800 2230 1407 2798
[37,] 1296 1075 836 94
[38,] 1325 2761 1422 1066
[39,] 143 33 62 110
[40,] 15 67 25 5
[41,] . . 1 .
[42,] 971 103 237 712
[43,] . 1 . .
[44,] . 5 5 5
[45,] 44 337 101 237
[46,] 30 101 16 164
[47,] 110 287 27 .
[48,] . . . 25
[49,] . . 1 .
[50,] 1320 6762 1628 8768
[51,] 302 1037 303 1405
[52,] . 52 6 111
[53,] . 99 17 256
[54,] 6 59 28 .
[55,] 1019 1933 364 110
[56,] . . 20 .
[57,] 244 522 201 4970
[58,] 2092 2551 8512 2179
[59,] 29 16 14 9
[60,] . 14 13 .
[61,] . . . 1
[62,] 30 95 29 .
[63,] . 5 . .
[64,] 34 752 285 152
[65,] . 6 3 102
[66,] 2 25 17 111
[67,] . 43 19 38
[68,] 432 67 155 314
[69,] 443 62 185 292
[70,] . 34 6 44
[71,] . 45 25 28
[72,] . 24 2 .
[73,] . 45 5 .
[74,] . 35 . .
[75,] 43 249 75 125
[76,] 4 10 1 5
[77,] 6 51 . 45
[78,] 18 50 13 87
[79,] . . . 2
[80,] . . 1 .
[81,] 105 276 60 7
[82,] . 41 25 .
[83,] 4 40 . 27
[84,] 2530 7101 1832 713
[85,] 661 1823 662 1071
[86,] . 1 1 1
[87,] . 3 . .
[88,] 103 . . .
[89,] 154 711 169 1041
[90,] 7 5 5 .
[91,] . 5 . .
[92,] 296 2559 619 3118
[93,] . 45 . .
[94,] . 25 . .
[95,] . 80 . .
[96,] . 199 22 .
[97,] 5064 20121 10158 2157
[98,] 20 89 12 29
[99,] 586 71 116 160
[100,] . . 4 .
[101,] 3489 29862 2629 7688
[102,] 56 171 49 19
[103,] . 27 . 24
[104,] 28 354 74 449
[105,] 162 21 51 120
[106,] 90 17 . .
[107,] 99 49 85 79
[108,] . 236 30 .
[109,] 17 124 40 177
[110,] . 3 3 9
[111,] 5 58 . .
[112,] 62 203 37 .
[113,] 20 44 . .
[114,] 105 336 173 289
[115,] 79 246 97 554
[116,] 1 . 4 .
[117,] . 49 . .
[118,] . 2 . .
[119,] 2 . . .
[120,] . 16 1 .
[121,] 69 133 43 23
[122,] 3 82 17 72
[123,] . 14 4 19
[124,] 7 34 9 .
[125,] 37 141 37 .
[126,] 418 61 160 266
[127,] . 33 . .
[128,] 483 89 140 386
[129,] 724 71 193 447
[130,] . 21 . .
[131,] 1004 3492 913 4543
[132,] 630 1870 600 2263
[133,] . 3 . .
[134,] 20 112 19 19
[135,] 3 21 11 .
[136,] 54 . . .
[137,] 24 34 23 38
[138,] 628 9095 1575 2738
[139,] 84 152 69 148
[140,] 228 708 278 478
[141,] . . 3 .
[142,] . 3 . .
[143,] . 30 8 .
[144,] 8 80 4 102
[145,] 3 30 . 56
[146,] 2 68 5 41
[147,] . . 5 .
[148,] . 20 8 .
[149,] 4 19 . .
[150,] 23 57 24 .
[151,] . 18 3 .
[152,] 7 101 5 .
[153,] 58 184 14 .
[154,] . . 3 .
[155,] 134 357 96 8
[156,] . . 2 .
[157,] 841 103 336 574
[158,] 15166 1081 9530 2880
[159,] 507 60 208 312
[160,] 361 17893 484 154
[161,] 11 34 10 .
[162,] 993 257 520 715
[163,] 17 75 11 87
[164,] 16 687 28 6
[165,] . 106 10 32
[166,] 216 117 72 133
[167,] . . 3 .
[168,] . . 8 108
[169,] 4 14 8 47
[170,] 6 15 . .
[171,] 6401 137578 45957 426
[172,] 138 382 80 28
[173,] . 26 8 20
[174,] 727 210 479 514
[175,] 622 121 259 536
[176,] 392 89 129 267
[177,] . 95 12 41
[178,] 24 324 58 .
[179,] . 43 28 .
[180,] 260 645 128 19
[181,] 226 660 176 861
[182,] 7 11 2 .
[183,] . . 5 .
[184,] 36753 81112 22611 694
[185,] 22 47 . 89
[186,] 184 1007 257 2212
[187,] 371 1910 427 1954
[188,] . . 2 .
[189,] 25 94 28 31
[190,] . . . 3
[191,] . 20 5 .
[192,] 34 128 13 .
[193,] 5 83 10 48
[194,] . 5 . .
[195,] . 20 117 338
[196,] 32 . . .
[197,] 869 9181 1891 6238
[198,] 2879 9543 6488 172123
[199,] 2 12 3 19
[200,] 685 93 227 614
[201,] 1426 158 397 1032
[202,] . . 1 .
[203,] 55 138 39 4
[204,] 818 2372 414 76
[205,] 497 137 341 417
[206,] 31 125 27 .
[207,] 3 20 6 .
[208,] . . 1 .
[209,] . 41 13 .
[210,] 128 147 42 70
[211,] 210 380 101 105
[212,] 287 729 131 .
[213,] 122 122 50 .
[214,] 29 . . .
[215,] . 13 . .
[216,] 27 197 52 157
[217,] 15 21 . .
[218,] 167 1152 304 1926
[219,] . . 1 28
[220,] 810 117 273 711
[221,] . . 2 .
[222,] . 2 . .
[223,] . . 4 .
[224,] . 17 24 31
[225,] 232 1006 222 76
[226,] 74 158 27 263
[227,] . 19 10 .
[228,] 223 883 267 533
[229,] 52 87 25 36
[230,] 340 613 488 2536
[231,] 182 849 272 521
[232,] 53726 55537 44625 29182
[233,] 2167 369 753 1293
[234,] 206 48 75 .
[235,] 62 2 . .
[236,] . . 1 .
[237,] 55 226 69 384
[238,] . 32 14 67
[239,] . 66 17 .
[240,] 18 249 70 321
[241,] . 2 . .
[242,] . 2 . .
[243,] 3 34 . 44
[244,] 155 830 173 1628
[245,] 36 466 70 589
[246,] . 17 4 33
[247,] . 16 . .
[248,] . 9 11 .
[249,] 167 26 62 105
[250,] . . . 4
[251,] . . 2 .
[252,] 1 81 33 92
[253,] 107 46 3 .
[254,] . 9 2 .
[255,] . 16 . .
[256,] . 22 . .
[257,] . 1 4 .
[258,] 136 23 69 70
[259,] 5095 44147 7578 70276
[260,] . . 11 .
[261,] . 82 . 117
[262,] 647 2017 382 166
[263,] 6 20 . .
[264,] . 6 . .
[265,] 5 174 33 .
[266,] 311 543 115 44
BIOM.utils documentation built on May 1, 2019, 7:32 p.m.
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Description Usage Arguments Details Value Author(s) References See Also Examples
Description
Convert an object of class biom into a basic type: matrix, list, or character.
Usage
1 2 3 4 5 6 7 8 |
Arguments
x |
an object ( |
expand |
if sparse, force return of not sparse matrix? ( |
... |
unused |
file |
filename for writing object |
Details
BIOM (Biological Observation Matrix) is a simple prescription for storing an annotated table of data. It may be described as a format, standard, or data structure.
The JSON (JavaScript Object Notation) standard for expressing general data objects as text is employed to define BIOM. Therefore the native form of BIOM data is structured text, conforming to the JSON specification in general and the BIOM specification in particular. Familiarity with BIOM is assumed here.
The S3 class biom and its methods facilitate analyses
by expressing BIOM data as objects in the R environment.
Each function above transforms an object that is
already of class biom into a basic R type.
as.matrix() returns the BIOM data table as a matrix.
If the object is "dense", then dimnames() of the result
are equal to the BIOM row and column ids.
Otherwise, the three-column sparse representation matrix is returned,
with ids given by attached attributes "rownames" and "colnames".
However, using expand=TRUE expands a sparse representation.
(Setting expand=FALSE has no effect when the object is "dense".)
Also, see below for an example using class "sparseMatrix"
from the R package Matrix.
as.character() returns BIOM properly speaking, that is,
data and annotations written in JSON text conforming to the BIOM specification.
That text is written to file, if provided.
See below for an example of saving the data table, only, in CSV or TSV format.
Of course, it is possible to bring biom objects
in and out of the session with save() and load().
as.list() returns a list corresponding closely
element-by-element to BIOM. The differences are:
list element data is a matrix not list;
elements rows and columns hold metadata only,
and so do not include ids; instead, additional elements
row.ids and column.ids are present;
and format_url is missing.
Value
For as.matrix() and as.list(), as described.
For as.character(), a single string of JSON text,
or simply file if it is not NULL.
Except that last case, these functions return invisibly.
Author(s)
Daniel T. Braithwaite
References
See Also
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | tt <- tempfile()
xx <- biom (li3)
yy <- biom (smat, sparse=TRUE, quiet=TRUE)
## extract objects of basic types:
print (as.matrix (xx))
head (as.matrix (yy, expand=TRUE))
as.character (xx)
as.character (xx, file=tt)
str (as.list (xx))
## export to a CSV file:
write.table (as.matrix (xx), file=tt, sep=",")
## Not run:
## a classed sparse matrix (for computation or what have you):
zz <- as.matrix (yy)
zz[,1:2] <- 1 + zz[,1:2]
Matrix::sparseMatrix (i=zz[,1], j=zz[,2], x=zz[,3])
## End(Not run)
unlink(tt)
|
Example output
BIOM.utils (0.9 dbcb27)
AAA BBB CCC DDD EEE
aaa 101 121 141 161 181
bbb 102 122 142 162 182
ccc 103 123 143 163 183
ddd 104 124 144 164 184
eee 105 125 145 165 185
fff 106 126 146 166 186
ggg 107 127 147 167 187
hhh 108 128 148 168 188
iii 109 129 149 169 189
jjj 110 130 150 170 190
kkk 111 131 151 171 191
lll 112 132 152 172 192
mmm 113 133 153 173 193
nnn 114 134 154 174 194
ooo 115 135 155 175 195
ppp 116 136 156 176 196
qqq 117 137 157 177 197
rrr 118 138 158 178 198
sss 119 139 159 179 199
ttt 120 140 160 180 200
column1 column2 column3 column4
row1 63 140 27 11
row2 11 37 0 75
row3 160 1025 151 2172
row4 0 0 4 0
row5 0 67 6 0
row6 0 38 13 0
[1] "{\n \"id\": \"\",\n\"format\": \"Biological Observation Matrix 1.0\",\n\"type\": \"OTU table\",\n\"generated_by\": \"BIOM.utils (0.9)\",\n\"date\": \"2017-12-14 17:01:08\",\n\"rows\": [\n {\n \"id\": \"aaa\",\n\"metadata\": \"metadata of aaa\" \n},\n{\n \"id\": \"bbb\",\n\"metadata\": \"metadata of bbb\" \n},\n{\n \"id\": \"ccc\",\n\"metadata\": \"metadata of ccc\" \n},\n{\n \"id\": \"ddd\",\n\"metadata\": \"metadata of ddd\" \n},\n{\n \"id\": \"eee\",\n\"metadata\": \"metadata of eee\" \n},\n{\n \"id\": \"fff\",\n\"metadata\": \"metadata of fff\" \n},\n{\n \"id\": \"ggg\",\n\"metadata\": \"metadata of ggg\" \n},\n{\n \"id\": \"hhh\",\n\"metadata\": \"metadata of hhh\" \n},\n{\n \"id\": \"iii\",\n\"metadata\": \"metadata of iii\" \n},\n{\n \"id\": \"jjj\",\n\"metadata\": \"metadata of jjj\" \n},\n{\n \"id\": \"kkk\",\n\"metadata\": \"metadata of kkk\" \n},\n{\n \"id\": \"lll\",\n\"metadata\": \"metadata of lll\" \n},\n{\n \"id\": \"mmm\",\n\"metadata\": \"metadata of mmm\" \n},\n{\n \"id\": \"nnn\",\n\"metadata\": \"metadata of nnn\" \n},\n{\n \"id\": \"ooo\",\n\"metadata\": \"metadata of ooo\" \n},\n{\n \"id\": \"ppp\",\n\"metadata\": \"metadata of ppp\" \n},\n{\n \"id\": \"qqq\",\n\"metadata\": \"metadata of qqq\" \n},\n{\n \"id\": \"rrr\",\n\"metadata\": \"metadata of rrr\" \n},\n{\n \"id\": \"sss\",\n\"metadata\": \"metadata of sss\" \n},\n{\n \"id\": \"ttt\",\n\"metadata\": \"metadata of ttt\" \n} \n],\n\"columns\": [\n {\n \"id\": \"AAA\",\n\"metadata\": \"metadata of AAA\" \n},\n{\n \"id\": \"BBB\",\n\"metadata\": \"metadata of BBB\" \n},\n{\n \"id\": \"CCC\",\n\"metadata\": \"metadata of CCC\" \n},\n{\n \"id\": \"DDD\",\n\"metadata\": \"metadata of DDD\" \n},\n{\n \"id\": \"EEE\",\n\"metadata\": \"metadata of EEE\" \n} \n],\n\"matrix_type\": \"dense\",\n\"matrix_element_type\": \"int\",\n\"shape\": [ 20, 5 ],\n\"data\": [\n [ 101, 121, 141, 161, 181 ],\n[ 102, 122, 142, 162, 182 ],\n[ 103, 123, 143, 163, 183 ],\n[ 104, 124, 144, 164, 184 ],\n[ 105, 125, 145, 165, 185 ],\n[ 106, 126, 146, 166, 186 ],\n[ 107, 127, 147, 167, 187 ],\n[ 108, 128, 148, 168, 188 ],\n[ 109, 129, 149, 169, 189 ],\n[ 110, 130, 150, 170, 190 ],\n[ 111, 131, 151, 171, 191 ],\n[ 112, 132, 152, 172, 192 ],\n[ 113, 133, 153, 173, 193 ],\n[ 114, 134, 154, 174, 194 ],\n[ 115, 135, 155, 175, 195 ],\n[ 116, 136, 156, 176, 196 ],\n[ 117, 137, 157, 177, 197 ],\n[ 118, 138, 158, 178, 198 ],\n[ 119, 139, 159, 179, 199 ],\n[ 120, 140, 160, 180, 200 ] \n],\n\"format_url\": {\n \"Biological Observation Matrix 1.0\": \"http://biom-format.org/documentation/format_versions/biom-1.0.html\" \n} \n}"
[1] "/work/tmp/tmp/RtmpCft7t2/filee0220dec3d4"
List of 14
$ id : chr ""
$ format : chr "Biological Observation Matrix 1.0"
$ type : chr "OTU table"
$ generated_by : chr "BIOM.utils (0.9)"
$ date : chr "2017-12-14 17:01:08"
$ rows :List of 20
..$ : chr "metadata of aaa"
..$ : chr "metadata of bbb"
..$ : chr "metadata of ccc"
..$ : chr "metadata of ddd"
..$ : chr "metadata of eee"
..$ : chr "metadata of fff"
..$ : chr "metadata of ggg"
..$ : chr "metadata of hhh"
..$ : chr "metadata of iii"
..$ : chr "metadata of jjj"
..$ : chr "metadata of kkk"
..$ : chr "metadata of lll"
..$ : chr "metadata of mmm"
..$ : chr "metadata of nnn"
..$ : chr "metadata of ooo"
..$ : chr "metadata of ppp"
..$ : chr "metadata of qqq"
..$ : chr "metadata of rrr"
..$ : chr "metadata of sss"
..$ : chr "metadata of ttt"
$ columns :List of 5
..$ : chr "metadata of AAA"
..$ : chr "metadata of BBB"
..$ : chr "metadata of CCC"
..$ : chr "metadata of DDD"
..$ : chr "metadata of EEE"
$ row.ids : chr [1:20] "aaa" "bbb" "ccc" "ddd" ...
$ column.ids : chr [1:5] "AAA" "BBB" "CCC" "DDD" ...
$ matrix_type : chr "dense"
$ matrix_element_type: chr "int"
$ shape : int [1:2] 20 5
$ data : int [1:20, 1:5] 101 102 103 104 105 106 107 108 109 110 ...
..- attr(*, "dimnames")=List of 2
.. ..$ : chr [1:20] "aaa" "bbb" "ccc" "ddd" ...
.. ..$ : chr [1:5] "AAA" "BBB" "CCC" "DDD" ...
$ comment : NULL
266 x 4 sparse Matrix of class "dgCMatrix"
[1,] 63 140 27 11
[2,] 11 37 . 75
[3,] 160 1025 151 2172
[4,] . . 4 .
[5,] . 67 6 .
[6,] . 38 13 .
[7,] 158 26 55 113
[8,] 15561 3511 4139 14627
[9,] 260 631 247 694
[10,] 109 401 124 95
[11,] 411 880 174 144
[12,] 37 255 28 5
[13,] 31 111 18 168
[14,] 122 469 71 32
[15,] . . 12 1
[16,] . 3 . .
[17,] . 2 2 .
[18,] 7 127 24 153
[19,] . 2 1 5
[20,] 4 8 7 .
[21,] 764 3647 909 3559
[22,] 2256 11759 3915 27659
[23,] 2 20 . 10
[24,] . 11 7 .
[25,] . 51 3 .
[26,] 886 119 230 755
[27,] 856 443 402 7924
[28,] 8 52 15 11
[29,] 122 . . .
[30,] 30 236 48 295
[31,] 61 236 101 47
[32,] . 15 . .
[33,] 496 58 209 268
[34,] 59 106 34 53
[35,] 1696 4431 881 195
[36,] 800 2230 1407 2798
[37,] 1296 1075 836 94
[38,] 1325 2761 1422 1066
[39,] 143 33 62 110
[40,] 15 67 25 5
[41,] . . 1 .
[42,] 971 103 237 712
[43,] . 1 . .
[44,] . 5 5 5
[45,] 44 337 101 237
[46,] 30 101 16 164
[47,] 110 287 27 .
[48,] . . . 25
[49,] . . 1 .
[50,] 1320 6762 1628 8768
[51,] 302 1037 303 1405
[52,] . 52 6 111
[53,] . 99 17 256
[54,] 6 59 28 .
[55,] 1019 1933 364 110
[56,] . . 20 .
[57,] 244 522 201 4970
[58,] 2092 2551 8512 2179
[59,] 29 16 14 9
[60,] . 14 13 .
[61,] . . . 1
[62,] 30 95 29 .
[63,] . 5 . .
[64,] 34 752 285 152
[65,] . 6 3 102
[66,] 2 25 17 111
[67,] . 43 19 38
[68,] 432 67 155 314
[69,] 443 62 185 292
[70,] . 34 6 44
[71,] . 45 25 28
[72,] . 24 2 .
[73,] . 45 5 .
[74,] . 35 . .
[75,] 43 249 75 125
[76,] 4 10 1 5
[77,] 6 51 . 45
[78,] 18 50 13 87
[79,] . . . 2
[80,] . . 1 .
[81,] 105 276 60 7
[82,] . 41 25 .
[83,] 4 40 . 27
[84,] 2530 7101 1832 713
[85,] 661 1823 662 1071
[86,] . 1 1 1
[87,] . 3 . .
[88,] 103 . . .
[89,] 154 711 169 1041
[90,] 7 5 5 .
[91,] . 5 . .
[92,] 296 2559 619 3118
[93,] . 45 . .
[94,] . 25 . .
[95,] . 80 . .
[96,] . 199 22 .
[97,] 5064 20121 10158 2157
[98,] 20 89 12 29
[99,] 586 71 116 160
[100,] . . 4 .
[101,] 3489 29862 2629 7688
[102,] 56 171 49 19
[103,] . 27 . 24
[104,] 28 354 74 449
[105,] 162 21 51 120
[106,] 90 17 . .
[107,] 99 49 85 79
[108,] . 236 30 .
[109,] 17 124 40 177
[110,] . 3 3 9
[111,] 5 58 . .
[112,] 62 203 37 .
[113,] 20 44 . .
[114,] 105 336 173 289
[115,] 79 246 97 554
[116,] 1 . 4 .
[117,] . 49 . .
[118,] . 2 . .
[119,] 2 . . .
[120,] . 16 1 .
[121,] 69 133 43 23
[122,] 3 82 17 72
[123,] . 14 4 19
[124,] 7 34 9 .
[125,] 37 141 37 .
[126,] 418 61 160 266
[127,] . 33 . .
[128,] 483 89 140 386
[129,] 724 71 193 447
[130,] . 21 . .
[131,] 1004 3492 913 4543
[132,] 630 1870 600 2263
[133,] . 3 . .
[134,] 20 112 19 19
[135,] 3 21 11 .
[136,] 54 . . .
[137,] 24 34 23 38
[138,] 628 9095 1575 2738
[139,] 84 152 69 148
[140,] 228 708 278 478
[141,] . . 3 .
[142,] . 3 . .
[143,] . 30 8 .
[144,] 8 80 4 102
[145,] 3 30 . 56
[146,] 2 68 5 41
[147,] . . 5 .
[148,] . 20 8 .
[149,] 4 19 . .
[150,] 23 57 24 .
[151,] . 18 3 .
[152,] 7 101 5 .
[153,] 58 184 14 .
[154,] . . 3 .
[155,] 134 357 96 8
[156,] . . 2 .
[157,] 841 103 336 574
[158,] 15166 1081 9530 2880
[159,] 507 60 208 312
[160,] 361 17893 484 154
[161,] 11 34 10 .
[162,] 993 257 520 715
[163,] 17 75 11 87
[164,] 16 687 28 6
[165,] . 106 10 32
[166,] 216 117 72 133
[167,] . . 3 .
[168,] . . 8 108
[169,] 4 14 8 47
[170,] 6 15 . .
[171,] 6401 137578 45957 426
[172,] 138 382 80 28
[173,] . 26 8 20
[174,] 727 210 479 514
[175,] 622 121 259 536
[176,] 392 89 129 267
[177,] . 95 12 41
[178,] 24 324 58 .
[179,] . 43 28 .
[180,] 260 645 128 19
[181,] 226 660 176 861
[182,] 7 11 2 .
[183,] . . 5 .
[184,] 36753 81112 22611 694
[185,] 22 47 . 89
[186,] 184 1007 257 2212
[187,] 371 1910 427 1954
[188,] . . 2 .
[189,] 25 94 28 31
[190,] . . . 3
[191,] . 20 5 .
[192,] 34 128 13 .
[193,] 5 83 10 48
[194,] . 5 . .
[195,] . 20 117 338
[196,] 32 . . .
[197,] 869 9181 1891 6238
[198,] 2879 9543 6488 172123
[199,] 2 12 3 19
[200,] 685 93 227 614
[201,] 1426 158 397 1032
[202,] . . 1 .
[203,] 55 138 39 4
[204,] 818 2372 414 76
[205,] 497 137 341 417
[206,] 31 125 27 .
[207,] 3 20 6 .
[208,] . . 1 .
[209,] . 41 13 .
[210,] 128 147 42 70
[211,] 210 380 101 105
[212,] 287 729 131 .
[213,] 122 122 50 .
[214,] 29 . . .
[215,] . 13 . .
[216,] 27 197 52 157
[217,] 15 21 . .
[218,] 167 1152 304 1926
[219,] . . 1 28
[220,] 810 117 273 711
[221,] . . 2 .
[222,] . 2 . .
[223,] . . 4 .
[224,] . 17 24 31
[225,] 232 1006 222 76
[226,] 74 158 27 263
[227,] . 19 10 .
[228,] 223 883 267 533
[229,] 52 87 25 36
[230,] 340 613 488 2536
[231,] 182 849 272 521
[232,] 53726 55537 44625 29182
[233,] 2167 369 753 1293
[234,] 206 48 75 .
[235,] 62 2 . .
[236,] . . 1 .
[237,] 55 226 69 384
[238,] . 32 14 67
[239,] . 66 17 .
[240,] 18 249 70 321
[241,] . 2 . .
[242,] . 2 . .
[243,] 3 34 . 44
[244,] 155 830 173 1628
[245,] 36 466 70 589
[246,] . 17 4 33
[247,] . 16 . .
[248,] . 9 11 .
[249,] 167 26 62 105
[250,] . . . 4
[251,] . . 2 .
[252,] 1 81 33 92
[253,] 107 46 3 .
[254,] . 9 2 .
[255,] . 16 . .
[256,] . 22 . .
[257,] . 1 4 .
[258,] 136 23 69 70
[259,] 5095 44147 7578 70276
[260,] . . 11 .
[261,] . 82 . 117
[262,] 647 2017 382 166
[263,] 6 20 . .
[264,] . 6 . .
[265,] 5 174 33 .
[266,] 311 543 115 44
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