# Load mia R package
library(mia)
# Load example data
data(HintikkaXOData)
mae <- HintikkaXOData
tse <- mae[["microbiota"]]
# Check column data for this data object
colData(tse)DataFrame with 40 rows and 0 columnsSummarizedExperiment
Data wrangling: SummarizedExperiment
SummarizedExperiment
Basic data operations
Extracting elements
Subsetting
Components
-> See the example solutions.
Example: colData
Example: rowData
DataFrame with 12706 rows and 7 columns
Phylum Class
<character> <character>
GAYR01026362.62.2014 D_1__Proteobacteria D_2__Alphaproteobact..
CVJT01000011.50.2173 D_1__Firmicutes D_2__Bacilli
KF625183.1.1786 D_1__Proteobacteria D_2__Gammaproteobact..
AYSG01000002.292.2076 D_1__Firmicutes D_2__Bacilli
CCPS01000022.154.1916 D_1__Proteobacteria D_2__Gammaproteobact..
... ... ...
JRJTB:03786:02940 D_1__Verrucomicrobia D_2__Verrucomicrobiae
JRJTB:03786:03034 D_1__Firmicutes D_2__Clostridia
JRJTB:03787:02353 D_1__Firmicutes D_2__Clostridia
JRJTB:03787:02429 D_1__Bacteroidetes D_2__Bacteroidia
JRJTB:03787:02478 D_1__Bacteroidetes D_2__Bacteroidia
Order Family
<character> <character>
GAYR01026362.62.2014 D_3__Rickettsiales D_4__Mitochondria
CVJT01000011.50.2173 D_3__Bacillales D_4__Staphylococcaceae
KF625183.1.1786 D_3__Enterobacteriales D_4__Enterobacteriac..
AYSG01000002.292.2076 D_3__Lactobacillales D_4__Streptococcaceae
CCPS01000022.154.1916 D_3__Enterobacteriales D_4__Enterobacteriac..
... ... ...
JRJTB:03786:02940 D_3__Verrucomicrobia.. D_4__Akkermansiaceae
JRJTB:03786:03034 D_3__Clostridiales D_4__Ruminococcaceae
JRJTB:03787:02353 D_3__Clostridiales D_4__Family XIII
JRJTB:03787:02429 D_3__Bacteroidales D_4__Muribaculaceae
JRJTB:03787:02478 D_3__Bacteroidales D_4__Muribaculaceae
Genus Species
<character> <character>
GAYR01026362.62.2014 D_5__Solanum melonge.. D_6__Solanum melonge..
CVJT01000011.50.2173 D_5__Staphylococcus D_6__Staphylococcus ..
KF625183.1.1786 D_5__Klebsiella D_6__Klebsiella oxyt..
AYSG01000002.292.2076 D_5__Streptococcus D_6__Streptococcus t..
CCPS01000022.154.1916 D_5__Escherichia-Shi.. D_6__Escherichia coli
... ... ...
JRJTB:03786:02940 D_5__Akkermansia NA
JRJTB:03786:03034 D_5__Ruminococcaceae.. D_6__uncultured bact..
JRJTB:03787:02353 D_5__Family XIII AD3.. D_6__uncultured bact..
JRJTB:03787:02429 D_5__uncultured bact.. D_6__uncultured bact..
JRJTB:03787:02478 D_5__uncultured bact.. D_6__uncultured bact..
OTU
<character>
GAYR01026362.62.2014 GAYR01026362.62.2014
CVJT01000011.50.2173 CVJT01000011.50.2173
KF625183.1.1786 KF625183.1.1786
AYSG01000002.292.2076 AYSG01000002.292.2076
CCPS01000022.154.1916 CCPS01000022.154.1916
... ...
JRJTB:03786:02940 JRJTB:03786:02940
JRJTB:03786:03034 JRJTB:03786:03034
JRJTB:03787:02353 JRJTB:03787:02353
JRJTB:03787:02429 JRJTB:03787:02429
JRJTB:03787:02478 JRJTB:03787:02478Transformations
- Presence/absence
- Compositional (percentages)
- \(Log_{10}\)
- CLR and other Aitchison transformations
- Phylogenetic transformations (e.g. philr)
- Custom transformations
Example: assays
C1 C2 C3 C4 C5 C6 C7 C8 C9
GAYR01026362.62.2014 0 0 0 0 0 0 0 0 0
CVJT01000011.50.2173 1 0 1 1 0 0 0 5 1
KF625183.1.1786 0 0 0 0 0 0 0 0 0
AYSG01000002.292.2076 0 0 0 0 1 0 0 0 0
CCPS01000022.154.1916 7 2 10 15 0 0 0 0 11
KJ923794.1.1762 0 0 0 0 0 0 0 0 0
CP006736.223921.225660 0 0 0 0 0 0 0 0 0
GEMN01027092.33.1623 0 0 0 0 0 0 0 0 0
EU622687.1.1587 0 23 14 43 9 5 2 21 8
KY646024.1.1591 0 0 2 0 0 0 0 0 0
JUOP01000215.81.1657 2 0 0 2 0 0 0 0 2
JN628990.1.1569 0 0 0 0 0 0 0 0 0
KF843412.1.1565 0 0 0 0 0 0 0 0 0
LG042641.312212.313771 4 1 65 94 29 23 32 7 79
AB559692.1.1569 0 0 1 0 0 0 0 0 0
AB559728.1.1569 0 0 0 0 0 0 0 0 0
KX960105.1.1558 0 0 0 0 0 0 0 0 0
AY349382.1.1568 21 3 152 94 28 42 54 10 204
AB559668.1.1567 0 0 0 0 0 0 0 0 0
AB606407.1.1554 0 18 0 0 0 0 0 1 19
AB969632.1.1565 0 0 0 2 0 0 1 0 3
DQ394600.1.1565 0 0 0 0 2 0 0 3 0
EU622770.1.1565 766 1510 1426 1245 1349 1171 1669 3337 3248
EU791072.1.1553 0 0 0 0 0 0 0 0 0
KF738665.1.1553 0 0 0 0 0 0 0 0 0
KU161106.1.1565 0 0 0 0 0 0 0 0 0
DQ394665.1.1563 0 0 0 0 0 0 0 0 0
DQ394662.1.1562 0 0 0 0 1 0 0 0 1
JQ805635.1.1591 0 0 0 0 0 0 0 0 0
AY858424.1.1561 0 4 1 2 1 0 0 0 4
DQ394666.1.1561 0 0 0 0 0 1 0 1 1
AF197125.1.1555 0 0 0 0 0 0 0 0 0
AM277369.1.1548 0 0 0 0 0 0 0 0 0
DQ105660.1.1557 0 0 0 4 0 0 0 0 0
DQ288684.1.1556 0 0 0 0 0 0 0 0 0
LQNG01000112.68.1642 0 0 0 0 0 0 0 0 0
AB506139.1.1558 0 0 0 0 0 0 0 0 0
AB507689.1.1558 0 0 0 0 0 0 0 0 0
AB606249.1.1546 0 9 18 16 2 3 0 4 13
AB824407.1.1559 0 0 0 0 0 0 0 0 0
DQ318870.1.1555 1 0 0 0 0 0 0 0 0
AB627542.1.1557 0 1 0 0 0 0 0 0 1
EU791265.1.1545 0 0 0 0 0 0 0 0 0
AATF01001055.137.1680 11 8 39 0 14 6 16 19 79
AY958894.1.1549 0 0 1 0 0 0 0 0 0
JQCN01000019.62.1605 0 0 0 0 0 0 0 0 0
KF476042.1.1565 0 0 0 0 0 0 0 0 0
AJ301839.1.1556 0 0 0 0 1 0 0 0 0
AB606326.1.1542 138 34 15 9 28 56 33 24 55
KJ833601.1.1542 0 0 1 0 0 0 0 0 0
AJAS01000002.402945.404493 0 0 0 0 0 0 0 0 0
AY941840.1.1568 1 2 0 0 0 0 0 0 0
FJ463818.1.1541 0 0 0 0 0 0 0 0 0
HK693990.17.1557 0 0 0 1 0 0 0 0 0
CP007394.148.1706 0 1 0 0 0 0 0 0 0
EF025907.1.1552 0 0 0 0 0 0 0 0 0
JFOF01000052.9721.11268 0 0 0 0 0 0 0 0 0
ACRY02000003.380006.381551 0 0 0 0 0 0 0 0 0
AJ242969.1.1539 0 0 0 0 0 0 0 0 0
CP015906.2140419.2141977 438 282 863 1503 617 755 251 294 1030
FJ951901.1.1538 2 5 2 4 5 7 7 14 12
CP012152.200511.202072 0 0 0 0 0 0 0 0 0
FJ879275.1.1537 0 0 2 0 1 3 1 1 3
GQ505032.1.1537 0 0 0 0 0 0 0 0 0
HM124144.1.1537 0 0 76 0 3 0 1 0 0
AB969423.1.1547 0 0 0 0 0 0 0 0 0
EU791219.1.1536 0 0 0 0 0 0 0 0 0
FJ880025.1.1536 0 0 0 0 0 0 0 0 0
AFST01000003.1612.3154 0 0 0 0 0 0 0 0 0
DQ288680.1.1547 0 1 5 0 0 0 0 0 0
DQ905283.1.1535 0 0 3 3 0 0 0 0 0
EF031001.1.1547 0 0 1 0 0 0 0 0 0
EU723854.1.1535 0 0 0 0 0 0 0 0 0
L23507.1.1535 0 0 0 0 0 0 0 0 0
AY959117.1.1537 0 0 0 0 0 0 0 0 0
EF406864.1.1535 0 0 4 1 0 0 0 0 0
EU845654.1.1551 0 0 1 3 0 0 5 2 0
DQ394661.1.1545 0 0 0 0 0 0 0 0 0
EF686530.1.1533 0 0 0 0 0 0 0 0 0
EU791081.1.1533 0 0 1 0 1 0 0 0 0
GQ451195.1.1535 0 0 0 0 0 2 2 2 2
AB606277.1.1532 1 0 9 3 0 0 0 0 2
EU791131.1.1532 0 0 1 0 0 0 0 0 0
HK555817.1.1532 0 0 0 0 0 0 0 0 0
JN713381.1.1544 0 1 6 1 3 5 2 4 6
JQ084715.1.1532 0 0 2 0 1 0 0 0 3
AB627471.1.1543 2 238 282 365 342 5 1401 1055 0
CDMW01000001.16532.18068 0 0 0 0 0 0 0 0 0
CDYJ01035375.5063.6592 0 0 0 0 0 0 0 0 0
FJ880194.1.1530 0 0 0 0 0 0 0 0 0
JN008436.1.1530 0 0 0 0 0 0 0 0 0
LC176070.1.1536 0 0 0 0 0 0 0 0 0
LN612693.1.1530 0 0 0 0 0 0 1 0 3
AF280866.1.1541 0 0 0 0 0 0 0 0 0
AY959035.1.1536 0 0 4 0 0 0 1 0 3
AYGZ01000001.327.1863 310 326 34 373 12 207 18 44 2
CP006776.2018563.2020110 0 0 0 0 0 0 0 0 0
CP019573.289123.290677 0 0 0 0 0 0 0 0 0
HM124277.1.1529 0 0 0 0 0 0 0 0 0
JX841323.1.1541 0 0 0 0 0 0 0 0 0
JX898154.1.1543 0 0 0 0 0 0 0 0 0
CP001918.5152784.5154334 2 0 0 3 6 2 0 5 3
CP007391.4812088.4813634 0 0 0 0 0 0 0 0 0
EU844697.1.1539 0 2 6 0 0 0 0 0 0
FJ879725.1.1573 1 0 0 0 0 0 0 0 0
HM124131.1.1528 0 0 0 0 0 0 0 0 0
JX218307.1.1528 0 0 0 0 0 0 0 0 0
M58839.1.1552 0 0 0 0 0 0 0 0 0
AB627729.1.1539 0 1 223 318 19 100 43 32 38
AB969334.1.1539 0 0 0 0 0 0 0 0 0
AIGU01000070.44831.46365 1 0 0 0 0 0 0 0 0
CZAB01000004.3636.5162 0 0 0 0 0 2 0 0 3
EU842501.1.1537 0 0 0 0 0 0 0 0 0
EU845426.1.1528 0 0 0 0 1 0 0 0 0
HM124053.1.1527 0 0 0 0 0 0 0 0 0
KC561105.1.1528 0 0 0 0 0 0 0 0 0
M58837.1.1552 0 0 0 0 0 0 0 0 0
AB976554.1.1526 0 0 0 0 0 0 0 0 0
DD361258.4.1529 0 0 0 0 0 0 0 0 0
GU084441.1.1526 0 0 0 0 0 0 0 0 0
HE681389.1.1540 0 0 0 0 0 0 0 0 0
JGZF01000005.1.1534 1 0 0 0 0 0 0 0 0
ABHO01000013.881.2425 0 0 0 0 0 0 0 0 0
EF603968.1.1525 42 18 15 23 18 39 28 16 22
EU622700.1.1525 0 0 0 0 0 0 0 0 1
JF712668.1.1525 0 0 0 0 0 0 0 0 0
KC561128.1.1525 0 0 0 0 0 0 0 0 0
ACQV01000002.9075.10620 0 0 0 0 0 0 0 0 0
ASTF01000015.433637.435168 0 2 1115 0 0 0 0 0 0
AY464464.1.1546 0 0 0 0 0 0 0 0 0
CP007391.155676.157218 0 0 0 0 0 0 0 0 0
GU303678.1.1524 0 0 1 0 0 0 0 0 0
JQ410832.1.1532 0 0 0 0 0 0 0 0 0
JX852667.1.1567 0 0 0 1 0 0 0 0 1
KX570900.1.1529 0 0 1 0 0 1 0 0 0
AB506445.1.1535 0 0 0 0 0 0 0 0 0
AF243154.1.1523 0 0 0 0 0 0 0 0 0
AF262239.1.1537 0 0 0 0 0 0 1 0 0
AIGO01000056.3386.4915 0 0 0 0 0 0 0 0 0
AIGU01000067.2664.4193 1 0 1 0 0 0 0 0 0
AWFQ01000007.543.2090 116 0 1 0 0 0 0 0 1
AXVO01000009.222.1744 0 0 0 0 0 0 0 0 0
AYMP01000037.63.1585 2 2 1 1 1 0 1 1 1
DQ229102.1.1535 0 0 0 0 0 0 0 0 0
EU791122.1.1523 0 0 0 0 0 0 2 1 0
FPLN01005933.9.1531 0 0 0 0 0 0 0 0 0
FPLN01010442.9.1531 0 0 0 0 0 0 0 0 0
GAIQ01048712.3375.4897 0 0 0 0 0 0 0 0 0
HK555632.10.1532 0 0 0 0 0 0 0 0 0
JN092599.1.1535 0 4 0 0 5 0 3 0 11
KC283052.1.1536 0 0 0 1 0 0 0 0 0
LZEX01000005.43.1590 0 0 0 0 0 0 0 0 0
AB118033.1.1533 0 0 0 0 0 0 0 0 1
AB855726.1.1526 0 0 0 1 0 0 0 0 0
AEZJ02000039.521.2062 0 0 0 0 0 0 0 0 0
AFUV01000004.339540.341080 0 0 0 0 0 0 0 0 0
CP015403.1369456.1371009 3841 1762 439 86 1626 1483 2485 1283 576
CP017665.1276159.1277680 1 0 0 0 0 0 0 0 0
DQ777942.1.1523 0 0 8 0 0 0 0 0 0
EF436433.1.1522 0 0 0 0 0 0 0 0 0
EF525539.1.1537 0 0 0 0 0 0 0 0 0
FPLN01000389.11.1532 0 0 0 0 0 0 0 0 0
FPLN01000546.8.1529 0 0 0 0 0 0 0 0 0
FPLN01000855.9.1530 0 0 0 0 0 0 0 0 0
FPLN01007699.15.1536 0 0 0 0 0 0 0 0 0
FPLN01008559.13.1534 0 0 0 0 0 0 0 0 0
FPLN01009130.13.1534 0 0 0 0 0 0 0 0 0
FPLN01009549.9.1530 0 0 0 0 0 0 0 0 0
FPLN01010122.33.1554 2 0 0 0 0 0 0 0 0
FPLP01001720.12.1533 0 0 0 0 0 0 0 0 0
FPLP01002800.10.1531 0 0 0 0 0 0 0 0 0
FPLP01005732.13.1534 0 0 0 0 0 0 0 0 0
HQ883938.1.1522 0 0 1 0 0 0 0 0 0
KF256028.1.1522 0 0 0 0 0 0 0 0 0
KF798716.1.1525 0 0 0 0 0 0 0 0 0
AB627641.1.1533 0 0 2 2 0 2 0 0 0
AB969408.1.1533 0 0 0 0 0 0 0 0 0
DQ444288.1.1533 1 0 0 0 0 0 0 0 0
EF406604.1.1522 59 234 50 69 69 89 40 42 29
FJ951905.1.1521 0 0 0 0 0 0 0 0 0
FPLN01008787.12.1532 0 0 0 0 0 0 0 0 0
FPLN01009100.13.1533 0 0 0 0 0 0 0 0 0
FPLN01009530.8.1528 0 0 0 0 0 0 0 0 0
FPLN01010390.8.1528 0 0 0 0 0 0 0 0 0
FPLP01000375.13.1533 0 0 0 0 0 0 0 0 0
FPLP01005029.13.1533 0 0 0 0 0 0 0 0 0
GFBH01086591.67.1587 0 0 0 0 0 0 0 0 0
GQ451294.1.1526 0 0 0 0 0 0 0 0 0
JN969333.1.1531 0 0 0 0 0 0 0 0 0
KF169839.1.1541 0 0 0 0 0 0 0 0 0
KU598985.1.1521 0 0 0 0 0 0 0 0 0
U90314.1.1541 0 0 0 0 0 0 0 0 0
AB438223.1.1521 0 0 0 0 0 0 0 0 0
AB626910.1.1521 0 0 0 1 0 0 0 0 0
AB661449.1.1532 0 0 0 0 0 0 0 0 0
ACTI01000029.29.1556 0 0 0 0 0 0 0 0 0
ASSW01000015.461351.462878 0 0 38 0 0 0 0 0 0
DQ360844.1.1532 0 0 0 0 0 0 0 0 0
FIZH01000008.70399.71918 0 0 0 0 0 0 0 0 0
FPLN01003342.15.1534 0 0 0 1 0 0 0 0 0
FPLN01004615.17.1536 0 0 0 0 0 0 0 0 0
HQ716224.1.1521 0 0 0 0 0 0 0 0 1
JQ711737.1.1532 0 0 0 0 0 0 0 1 0
KR068404.1.1520 0 0 0 0 0 0 0 0 1
AB606354.1.1519 1 0 66 111 0 0 1 0 0
AB702924.1.1524 0 0 23 0 0 0 5 0 0
AKCD01000001.321917.323435 1275 2790 305 337 357 2942 922 2024 1755
DQ905926.1.1529 8 4 0 2 2 2 1 0 2
EU843173.1.1540 0 3 0 33 4 1 3 1 10
KF621060.1.1519 0 0 0 0 0 0 0 0 0
AB627689.1.1530 0 0 0 0 0 0 0 0 2
CALK01000057.3384.4901 56 8 20 12 30 25 17 44 58
CBWN010000030.3384.4921 0 0 0 0 0 0 0 0 0
EF604619.1.1518 0 0 0 0 0 0 0 0 0
FMGP01000001.650541.652058 0 0 0 0 0 0 0 0 0
FPLM01003000.9.1526 0 0 0 0 0 0 0 0 0
FPLM01006183.13.1530 0 0 0 0 0 0 0 0 0
HQ883936.1.1518 0 0 0 0 0 0 0 0 0
HQ883940.1.1518 0 0 0 0 0 0 0 0 0
JN254645.1.1523 0 0 0 0 0 0 0 0 0
JX145037.1.1531 0 1 0 0 0 0 0 0 0
AB188790.1.1517 0 0 0 0 0 0 0 0 0
AB969619.1.1529 36 15 7 15 0 37 2 17 10
AF262236.1.1531 5 2 0 0 8 7 0 1 1
AY661991.1.1529 0 0 0 0 0 0 0 0 0
FJ172874.1.1517 0 0 0 0 0 0 0 0 0
FJ881220.1.1517 0 0 0 1 0 0 0 0 0
HQ883943.1.1517 0 0 0 0 0 0 0 0 0
AB627492.1.1527 155 94 244 301 66 647 214 243 306
AKNF01001123.2375.3897 0 0 0 0 0 0 0 0 0
BBXJ01000001.2660388.2661903 0 0 1 0 0 0 0 0 0
EF406671.1.1517 19 0 0 0 0 0 0 0 0
FJ957835.1.1517 0 0 0 0 0 0 0 0 0
FPLN01001151.8.1523 0 0 0 0 0 0 0 0 1
FPLO01000691.7.1522 90 114 11 6 64 144 155 314 45
AY587831.1.1515 0 0 0 0 0 0 0 0 0
AY958808.1.1523 0 0 0 0 0 0 0 0 0
BAHW02000064.49.1563 58 0 0 0 0 0 0 0 0
FMGA01000006.679.2193 0 0 0 0 1 0 0 0 0
FTYE01000020.375.1897 0 0 0 0 0 0 0 0 0
JX198656.1.1515 2 108 429 39 0 219 31 134 7
LN907736.1.1566 2 0 0 0 0 0 0 0 0
MLAJ01000016.155.1693 6 45 42 9 1 40 2 3 9
AB627687.1.1526 10 1286 1812 71 1377 296 706 1583 267
AB746536.1.1526 0 0 0 0 0 0 0 0 0
AB969479.1.1526 0 0 0 3 0 0 0 0 1
AF224303.1.1531 0 0 0 0 0 0 0 0 0
AQFT01000055.1196.2717 0 0 0 0 0 0 0 0 0
AY958891.1.1518 0 0 1 2 0 0 0 0 0
CP015400.1820588.1822127 18 2 12 6 2 1 5 0 3
EF031004.1.1524 0 0 0 0 0 0 0 0 0
EF071294.1.1520 0 0 0 0 0 0 0 0 0
EU622706.1.1514 0 0 0 2 0 0 0 0 0
FPLO01004147.8.1521 0 0 0 0 0 0 0 0 0
JN969340.1.1517 0 0 0 0 0 0 0 0 0
JX218620.1.1514 0 0 0 0 0 0 0 0 0
MKZZ01000031.48.1589 0 1 0 0 0 0 0 0 0
MLHG01000091.232.1769 0 0 0 0 0 0 0 0 0
MLHI01000090.51.1588 1 0 0 0 0 0 0 0 0
AB034064.1.1528 0 0 0 0 0 0 0 0 0
AB506181.1.1525 0 0 0 0 0 0 0 0 0
AB506423.1.1525 0 0 0 0 0 0 0 0 0
AB627487.1.1525 0 0 0 0 0 0 0 0 0
AB627500.1.1525 0 0 0 0 0 0 0 0 0
AB627509.1.1525 0 3 6 10 1 6 1 1 4
AB627520.1.1525 15 4 9 16 8 6 8 8 4
AB627586.1.1525 0 0 7 0 0 0 0 77 0
AB627599.1.1525 13 3 207 7 0 0 19 48 2
AB627601.1.1525 42 12 7 32 4 13 3 2 26
AB627609.1.1525 0 0 0 5 0 0 0 0 0
AB821699.1.1525 0 0 0 0 0 0 0 0 0
AB969366.1.1525 3 13 1 2 13 1 15 15 2
AB969483.1.1525 0 0 0 17 0 0 0 0 0
AB969643.1.1525 0 1 5 23 0 1 3 0 0
ABVQ01000037.56921.58441 0 0 0 2 0 0 0 2 7
AY854353.1.1525 0 0 0 0 0 0 0 0 0
CP015405.196247.197788 1 0 0 0 0 0 0 0 0
CVTZ01000011.472188.473700 0 0 0 0 0 1 0 0 0
CYYV01000001.321800.323312 3304 0 0 55 0 0 0 0 0
CZAC01000092.963.2475 0 0 0 0 0 0 0 0 0
DQ057436.1.1513 0 0 0 0 0 0 0 0 0
DQ777889.1.1539 0 0 0 1 0 0 0 0 0
EF406567.1.1514 0 0 0 0 0 0 0 0 0
EF603374.1.1513 0 0 0 0 0 0 1 0 4
FMFJ01000009.575.2087 0 0 0 0 0 0 0 0 5
GU985201.1.1526 0 0 0 0 0 0 0 0 0
LC028624.1.1525 0 0 0 0 1 0 0 0 3
AATC01000018.2.1513 0 0 10 18 0 0 2 0 0
AB506430.1.1524 0 0 0 0 0 0 0 0 0
AB606306.1.1512 0 0 1 0 0 0 0 0 0
AB627590.1.1524 0 0 0 0 0 0 0 0 0
AB969320.1.1524 0 0 0 0 0 0 0 0 0
AB969520.1.1523 43 439 74 5 297 476 406 240 156
ACTP02000009.47.1566 292 18 10 20 41 28 20 49 24
ACTP02000011.422074.423593 0 0 0 0 0 0 0 0 0
ADLO01000142.506.2025 598 43 0 4 19 50 15 81 49
AGYM01000049.26155.27674 0 0 0 0 0 0 0 0 0
AGYU01000014.10038.11557 0 0 0 0 0 0 0 0 0
AWST01000112.51.1570 0 0 0 0 0 0 0 0 0
AY792237.1.1524 0 0 0 0 0 0 0 0 0
CP007394.3516165.3517696 0 0 0 0 0 0 0 0 0
CP016448.1542496.1544014 0 0 0 0 0 0 0 0 0
EF025906.1.1521 217 48 2 2 29 12 31 4 8
EU791025.1.1513 0 0 0 0 0 0 0 0 0
FMGI01000008.23183.24694 0 0 0 0 0 0 0 0 0
FPLO01004733.18.1529 0 0 0 0 1 1 0 0 0
HK556912.2.1513 0 0 0 0 0 0 0 0 0
HL953773.1.1512 0 0 0 0 0 0 0 0 0
HW066464.1.1512 0 23 6 1 2 17 5 6 25
JN867384.1.1518 0 0 0 0 0 0 0 0 0
JPJD01000056.3683.5194 82 63 21 4 21 28 57 13 39
AAXA02000014.354465.355983 48 9 10 3 12 5 5 11 4
AB506422.1.1523 0 0 50 0 0 0 0 0 0
AB559603.1.1522 0 0 1 0 0 0 0 0 0
AB627664.1.1523 0 2 69 359 0 23 24 1 1
AB969484.1.1523 58 21 21 39 2 14 18 18 16
ADLR01000157.173.1691 13 239 31 1 110 67 29 474 323
CDTY01028331.429.1939 0 0 1 0 0 0 0 0 0
CDTY01055436.5943.7453 0 0 0 0 0 1 0 0 0
CP011391.1021283.1022806 0 0 1 0 0 0 0 2 0
CVUG01000013.3917.5427 0 0 1 1 1 0 0 1 0
EF445284.1.1511 0 0 0 0 0 0 0 0 0
FLKC01000014.123770.125280 108 0 0 0 0 0 0 0 0
FMET01000007.119434.120944 0 0 1 0 0 0 0 0 0
FNBY01000022.77090.78624 0 0 0 0 0 0 0 0 0
HK693827.8.1518 1 0 0 0 0 0 0 0 0
HK694229.2.1512 0 40 0 0 47 43 30 193 17
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[ reached getOption("max.print") -- omitted 10207 rows ]Task: explore the data
Use OMA to find out how to pick up the following from your example data, and explain what each of these elements represents.
colData
rowData
assays
Adding new assays & extracting assays
Add log10 or CLR transformation for the data (hint: transformAssay)
Visualize abundance of a selected feature w.r.t. sample metadata
Adding elements to colData
Calculate Shannon diversity and add to colData (hint: estimateDiversity)
Visualize diversity w.r.t. sample metadata
Further tasks
Importing your own data
Constructing TreeSE from scracth
Other OMA Exercises on data containers.
Overview so far
By now, you are supposed to be able to:
understand the basic structure of the TreeSE data container
extract specific components from the object (assays, sample & feature info, trees)
-> How to manipulate & operate with this data object?