Difference between revisions of "Data.table"
From kogic.kr
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<h3 style="color:#aaa; font-style:italic"><span style="font-family:courier new,courier,monospace">Input</span></h3> | <h3 style="color:#aaa; font-style:italic"><span style="font-family:courier new,courier,monospace">Input</span></h3> | ||
| − | <div style="background:#eee;border:1px solid #ccc;padding:5px 10px;"><span style="font- | + | <div style="background:#eee;border:1px solid #ccc;padding:5px 10px;"><span style="font-family:courier new,courier,monospace"><span style="font-size:11px"> Species ID Var1 Var2 Val Group Print_name<br /> |
1: Dendronephthya_gigantea g30906.t1.cds@g30906@000029F CDS_length Full 2.01600e+03 Non-symbiotic_cnidarian Carnation_coral<br /> | 1: Dendronephthya_gigantea g30906.t1.cds@g30906@000029F CDS_length Full 2.01600e+03 Non-symbiotic_cnidarian Carnation_coral<br /> | ||
2: Dendronephthya_gigantea g14782.t1.cds@g14782@000108F CDS_length Full 4.02000e+02 Non-symbiotic_cnidarian Carnation_coral<br /> | 2: Dendronephthya_gigantea g14782.t1.cds@g14782@000108F CDS_length Full 4.02000e+02 Non-symbiotic_cnidarian Carnation_coral<br /> | ||
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<h3 style="color:#aaa; font-style:italic"><span style="font-family:courier new,courier,monospace">Output</span></h3> | <h3 style="color:#aaa; font-style:italic"><span style="font-family:courier new,courier,monospace">Output</span></h3> | ||
| − | <div style="background:#eee;border:1px solid #ccc;padding:5px 10px;"><span style="font- | + | <div style="background:#eee;border:1px solid #ccc;padding:5px 10px;"><span style="font-family:courier new,courier,monospace"><span style="font-size:11px"> ID CDS_length FPKM<br /> |
1: g10.t1.cds@g10@000002F 1185 30.363500<br /> | 1: g10.t1.cds@g10@000002F 1185 30.363500<br /> | ||
2: g100.t1.cds@g100@000002F 696 0.959006<br /> | 2: g100.t1.cds@g100@000002F 696 0.959006<br /> | ||
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4: g10000.t1.cds@g10000@000064F 1074 0.278465<br /> | 4: g10000.t1.cds@g10000@000064F 1074 0.278465<br /> | ||
5: g10001.t1.cds@g10001@000064F 522 0.962268 </span></span></div> | 5: g10001.t1.cds@g10001@000064F 522 0.962268 </span></span></div> | ||
| + | |||
| + | <h1><span style="font-family:courier new,courier,monospace">Data table aggregation with 'by'</span></h1> | ||
| + | |||
| + | <h3 style="color:#aaa;font-style:italic;"><span style="font-family:courier new,courier,monospace">Input</span></h3> | ||
| + | |||
| + | <div style="background:#eee;border:1px solid #ccc;padding:5px 10px;"><span style="font-family:courier new,courier,monospace"><span style="font-size:11px"> ID CDS_length FPKM ord bin<br /> | ||
| + | 1: g10.t1.cds@g10@000002F 10.210671 4.9242662 10665 8<br /> | ||
| + | 2: g10002.t1.cds@g10002@000064F 12.039262 2.3361320 3975 3<br /> | ||
| + | 3: g10008.t1.cds@g10008@000073F 9.162391 0.6201266 856 1<br /> | ||
| + | 4: g10011.t1.cds@g10011@000073F 9.942515 1.9781956 3149 3<br /> | ||
| + | 5: g10012.t1.cds@g10012@000073F 10.762382 0.5596289 785 1</span></span></div> | ||
| + | |||
| + | <h3 style="color:#aaa;font-style:italic;"><span style="font-family:courier new,courier,monospace">Code</span></h3> | ||
| + | |||
| + | <div style="background:#eee;border:1px solid #ccc;padding:5px 10px;"><span style="font-family:courier new,courier,monospace"><big>dt[, .(Mean_CDS_length = mean(CDS_length), Mean_FPKM = mean(FPKM)), by=bin]</big></span></div> | ||
| + | |||
| + | <h3 style="color:#aaa;font-style:italic;"><span style="font-family:courier new,courier,monospace">Output</span></h3> | ||
| + | |||
| + | <div style="background:#eee;border:1px solid #ccc;padding:5px 10px;"><span style="font-family:courier new,courier,monospace"><span style="font-size:11px"> bin Mean_CDS_length Mean_FPKM<br /> | ||
| + | 1: 8 10.187520 4.7044951<br /> | ||
| + | 2: 3 10.590668 2.0831168<br /> | ||
| + | 3: 1 10.488467 0.4904325<br /> | ||
| + | 4: 4 10.550280 2.6412267<br /> | ||
| + | 5: 2 10.541246 1.3801430<br /> | ||
| + | 6: 7 10.344120 4.1326888<br /> | ||
| + | 7: 6 10.377043 3.6221557<br /> | ||
| + | 8: 10 9.563917 7.4570552<br /> | ||
| + | 9: 5 10.509382 3.1425986<br /> | ||
| + | 10: 9 9.941699 5.4668993</span></span></div> | ||
| + | |||
| + | <p> </p> | ||
Revision as of 16:23, 27 November 2018
Contents
Convert a molten data table into an data table (array type)
Input
Species ID Var1 Var2 Val Group Print_name
1: Dendronephthya_gigantea g30906.t1.cds@g30906@000029F CDS_length Full 2.01600e+03 Non-symbiotic_cnidarian Carnation_coral
2: Dendronephthya_gigantea g14782.t1.cds@g14782@000108F CDS_length Full 4.02000e+02 Non-symbiotic_cnidarian Carnation_coral
3: Dendronephthya_gigantea g9986.t1.cds@g9986@000064F CDS_length Full 8.40000e+02 Non-symbiotic_cnidarian Carnation_coral
4: Dendronephthya_gigantea g1279.t1.cds@g1279@000024F CDS_length Full 8.58000e+02 Non-symbiotic_cnidarian Carnation_coral
Code
dcast(dt, ID ~ Var1, value.var = "Val")
Output
ID CDS_length FPKM
1: g10.t1.cds@g10@000002F 1185 30.363500
2: g100.t1.cds@g100@000002F 696 0.959006
3: g1000.t1.cds@g1000@000011F 660 0.000000
4: g10000.t1.cds@g10000@000064F 1074 0.278465
Data table aggregation with 'by'
Input
ID CDS_length FPKM ord bin
1: g10.t1.cds@g10@000002F 10.210671 4.9242662 10665 8
2: g10002.t1.cds@g10002@000064F 12.039262 2.3361320 3975 3
3: g10008.t1.cds@g10008@000073F 9.162391 0.6201266 856 1
4: g10011.t1.cds@g10011@000073F 9.942515 1.9781956 3149 3
Code
dt[, .(Mean_CDS_length = mean(CDS_length), Mean_FPKM = mean(FPKM)), by=bin]
Output
bin Mean_CDS_length Mean_FPKM
1: 8 10.187520 4.7044951
2: 3 10.590668 2.0831168
3: 1 10.488467 0.4904325
4: 4 10.550280 2.6412267
5: 2 10.541246 1.3801430
6: 7 10.344120 4.1326888
7: 6 10.377043 3.6221557
8: 10 9.563917 7.4570552
9: 5 10.509382 3.1425986
