Latest revision as of 12:39, 24 January 2019

Convert a molten data table into an data table (array type)

Input (head)

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

5: Dendronephthya_gigantea g9325.t1.cds@g9325@000042F CDS_length Full 8.61000e+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

5: g10001.t1.cds@g10001@000064F 522 0.962268

Fast melt for Data table

Input (head)

Position G4-SV40 G4-SV40-OHT

1: 101488764 52 51
2: 101488765 52 50
3: 101488766 52 49
4: 101488767 53 49

5: 101488768 54 49

Code

melt(SeqDepth_dt, id.vars = "Position")

Output (head)

Position variable value

1: 101488764 G4-SV40 52
2: 101488765 G4-SV40 52
3: 101488766 G4-SV40 52
4: 101488767 G4-SV40 53

5: 101488768 G4-SV40 54

Data table aggregation with 'by'

Input (head)

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

5: g10012.t1.cds@g10012@000073F 10.762382 0.5596289 785 1

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

10: 9 9.941699 5.4668993

Data table row-wise calculation

Input (head)

Description ID Anolis_carolinensis Balaena_mysticetus Balaenoptera_acutorostrata_scammoni

1: OG000001 OG000001 126 103 107
2: OG000002 OG000002 70 19 48
3: OG000003 OG000003 27 29 25
4: OG000004 OG000004 39 36 47

5: OG000005 OG000005 1 11 3

Code

dt[,Sum := rowSums(.SD, na.rm=T), .SDcols = 3:5]

dt[,Mean := rowMeans(.SD, na.rm=T), .SDcols = 3:5]

Output

Description ID Anolis_carolinensis Balaena_mysticetus Balaenoptera_acutorostrata_scammoni Sum Avg

1: OG000001 OG000001 126 103 107 336 112.00000
2: OG000002 OG000002 70 19 48 137 45.66667
3: OG000003 OG000003 27 29 25 81 27.00000
4: OG000004 OG000004 39 36 47 122 40.66667

5: OG000005 OG000005 1 11 3 15 5.00000

@@ Line 3: / Line 3: @@
 <h1><span style="font-family:courier new,courier,monospace">Convert a molten data table into an data table (array type)</span></h1>
-<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 (head)</span></h3>
-<div style="background:#eee;border:1px solid #ccc;padding:5px 10px;"><span style="font-family:courier new,courier,monospace">&nbsp;&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;Species &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ID &nbsp; &nbsp; &nbsp; Var1 Var2 &nbsp; &nbsp; &nbsp; &nbsp; Val &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Group &nbsp; &nbsp; &nbsp;Print_name<br />
+<div style="background:#eee;border:1px solid #ccc;padding:5px 10px;"><span style="font-family:courier new,courier,monospace"><span style="font-size:11px">&nbsp;&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;Species &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ID &nbsp; &nbsp; &nbsp; Var1 Var2 &nbsp; &nbsp; &nbsp; &nbsp; Val &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Group &nbsp; &nbsp; &nbsp;Print_name<br />
 &nbsp; &nbsp; 1: Dendronephthya_gigantea g30906.t1.cds@g30906@000029F CDS_length Full 2.01600e+03 Non-symbiotic_cnidarian Carnation_coral<br />
 &nbsp; &nbsp; 2: Dendronephthya_gigantea g14782.t1.cds@g14782@000108F CDS_length Full 4.02000e+02 Non-symbiotic_cnidarian Carnation_coral<br />
 &nbsp; &nbsp; 3: Dendronephthya_gigantea &nbsp; g9986.t1.cds@g9986@000064F CDS_length Full 8.40000e+02 Non-symbiotic_cnidarian Carnation_coral<br />
 &nbsp; &nbsp; 4: Dendronephthya_gigantea &nbsp; g1279.t1.cds@g1279@000024F CDS_length Full 8.58000e+02 Non-symbiotic_cnidarian Carnation_coral<br />
-&nbsp; &nbsp; 5: Dendronephthya_gigantea &nbsp; g9325.t1.cds@g9325@000042F CDS_length Full 8.61000e+02 Non-symbiotic_cnidarian Carnation_coral</span></div>
+&nbsp; &nbsp; 5: Dendronephthya_gigantea &nbsp; g9325.t1.cds@g9325@000042F CDS_length Full 8.61000e+02 Non-symbiotic_cnidarian Carnation_coral</span></span></div>
 <h3 style="color:#aaa; font-style:italic"><span style="font-family:courier new,courier,monospace">Code</span></h3>
@@ Line 18: / Line 18: @@
 <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">&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;ID CDS_length &nbsp; &nbsp; &nbsp;FPKM<br />
+<div style="background:#eee;border:1px solid #ccc;padding:5px 10px;"><span style="font-family:courier new,courier,monospace"><span style="font-size:11px">&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;ID CDS_length &nbsp; &nbsp; &nbsp;FPKM<br />
 &nbsp; &nbsp; 1: &nbsp; &nbsp; &nbsp; g10.t1.cds@g10@000002F &nbsp; &nbsp; &nbsp; 1185 30.363500<br />
 &nbsp; &nbsp; 2: &nbsp; &nbsp; g100.t1.cds@g100@000002F &nbsp; &nbsp; &nbsp; &nbsp;696 &nbsp;0.959006<br />
 &nbsp; &nbsp; 3: &nbsp; g1000.t1.cds@g1000@000011F &nbsp; &nbsp; &nbsp; &nbsp;660 &nbsp;0.000000<br />
 &nbsp; &nbsp; 4: g10000.t1.cds@g10000@000064F &nbsp; &nbsp; &nbsp; 1074 &nbsp;0.278465<br />
-&nbsp; &nbsp; 5: g10001.t1.cds@g10001@000064F &nbsp; &nbsp; &nbsp; &nbsp;522 &nbsp;0.962268&nbsp; &nbsp;&nbsp;</span></div>
+&nbsp; &nbsp; 5: g10001.t1.cds@g10001@000064F &nbsp; &nbsp; &nbsp; &nbsp;522 &nbsp;0.962268&nbsp; &nbsp;&nbsp;</span></span></div>
+<h1><span style="font-family:courier new,courier,monospace">Fast melt for Data table</span></h1>
+<h3 style="color:#aaa; font-style:italic"><span style="font-family:courier new,courier,monospace">Input (head)</span></h3>
+<div style="background:#eee;border:1px solid #ccc;padding:5px 10px;"><span style="font-size:11px"><span style="font-family:courier new,courier,monospace">&nbsp; &nbsp; &nbsp; &nbsp; Position G4-SV40 G4-SV40-OHT<br />
+&nbsp; &nbsp; 1: 101488764 &nbsp; &nbsp; &nbsp;52 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;51<br />
+&nbsp; &nbsp; 2: 101488765 &nbsp; &nbsp; &nbsp;52 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;50<br />
+&nbsp; &nbsp; 3: 101488766 &nbsp; &nbsp; &nbsp;52 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;49<br />
+&nbsp; &nbsp; 4: 101488767 &nbsp; &nbsp; &nbsp;53 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;49<br />
+&nbsp; &nbsp; 5: 101488768 &nbsp; &nbsp; &nbsp;54 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;49</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;"><big><span style="font-family:courier new,courier,monospace">melt(SeqDepth_dt, id.vars = &quot;Position&quot;)</span></big></div>
+<h3 style="color:#aaa; font-style:italic"><span style="font-family:courier new,courier,monospace">Output (head)</span></h3>
+<div style="background:#eee;border:1px solid #ccc;padding:5px 10px;"><span style="font-size:11px"><span style="font-family:courier new,courier,monospace">&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;Position &nbsp; &nbsp;variable value<br />
+&nbsp; &nbsp; &nbsp;1: 101488764 &nbsp; &nbsp; G4-SV40 &nbsp; &nbsp;52<br />
+&nbsp; &nbsp; &nbsp;2: 101488765 &nbsp; &nbsp; G4-SV40 &nbsp; &nbsp;52<br />
+&nbsp; &nbsp; &nbsp;3: 101488766 &nbsp; &nbsp; G4-SV40 &nbsp; &nbsp;52<br />
+&nbsp; &nbsp; &nbsp;4: 101488767 &nbsp; &nbsp; G4-SV40 &nbsp; &nbsp;53<br />
+&nbsp; &nbsp; &nbsp;5: 101488768 &nbsp; &nbsp; G4-SV40 &nbsp; &nbsp;54</span></span></div>
+<h1><span style="font-family:courier new,courier,monospace">Data table aggregation with &#39;by&#39;</span></h1>
+<h3 style="color:#aaa; font-style:italic"><span style="font-family:courier new,courier,monospace">Input (head)</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">&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;ID CDS_length &nbsp; &nbsp; &nbsp;FPKM &nbsp; ord bin<br />
+&nbsp; &nbsp; 1: &nbsp; &nbsp; &nbsp; g10.t1.cds@g10@000002F &nbsp;10.210671 4.9242662 10665 &nbsp; 8<br />
+&nbsp; &nbsp; 2: g10002.t1.cds@g10002@000064F &nbsp;12.039262 2.3361320 &nbsp;3975 &nbsp; 3<br />
+&nbsp; &nbsp; 3: g10008.t1.cds@g10008@000073F &nbsp; 9.162391 0.6201266 &nbsp; 856 &nbsp; 1<br />
+&nbsp; &nbsp; 4: g10011.t1.cds@g10011@000073F &nbsp; 9.942515 1.9781956 &nbsp;3149 &nbsp; 3<br />
+&nbsp; &nbsp; 5: g10012.t1.cds@g10012@000073F &nbsp;10.762382 0.5596289 &nbsp; 785 &nbsp; 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">&nbsp; &nbsp; bin Mean_CDS_length Mean_FPKM<br />
+&nbsp;1: &nbsp; 8 &nbsp; &nbsp; &nbsp; 10.187520 4.7044951<br />
+&nbsp;2: &nbsp; 3 &nbsp; &nbsp; &nbsp; 10.590668 2.0831168<br />
+&nbsp;3: &nbsp; 1 &nbsp; &nbsp; &nbsp; 10.488467 0.4904325<br />
+&nbsp;4: &nbsp; 4 &nbsp; &nbsp; &nbsp; 10.550280 2.6412267<br />
+&nbsp;5: &nbsp; 2 &nbsp; &nbsp; &nbsp; 10.541246 1.3801430<br />
+&nbsp;6: &nbsp; 7 &nbsp; &nbsp; &nbsp; 10.344120 4.1326888<br />
+&nbsp;7: &nbsp; 6 &nbsp; &nbsp; &nbsp; 10.377043 3.6221557<br />
+&nbsp;8: &nbsp;10 &nbsp; &nbsp; &nbsp; &nbsp;9.563917 7.4570552<br />
+&nbsp;9: &nbsp; 5 &nbsp; &nbsp; &nbsp; 10.509382 3.1425986<br />
+: &nbsp; 9 &nbsp; &nbsp; &nbsp; &nbsp;9.941699 5.4668993</span></span></div>
+<h1><span style="font-family:courier new,courier,monospace">Data table row-wise calculation</span></h1>
+<h3 style="color:#aaa; font-style:italic"><span style="font-family:courier new,courier,monospace">Input (head)</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">&nbsp; &nbsp;Description &nbsp; &nbsp; &nbsp; ID Anolis_carolinensis Balaena_mysticetus Balaenoptera_acutorostrata_scammoni<br />
+: &nbsp; &nbsp;OG000001 OG000001 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 126 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;103 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 107<br />
+: &nbsp; &nbsp;OG000002 OG000002 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;70 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 19 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;48<br />
+: &nbsp; &nbsp;OG000003 OG000003 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;27 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 29 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;25<br />
+: &nbsp; &nbsp;OG000004 OG000004 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;39 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 36 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;47<br />
+: &nbsp; &nbsp;OG000005 OG000005 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 1 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 11 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 3</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[,Sum := rowSums(.SD, na.rm=T), .SDcols = 3:5]</big></span></div>
+<div style="background:#eee;border:1px solid #ccc;padding:5px 10px;"><span style="font-family:courier new,courier,monospace"><big>dt[,Mean&nbsp;:= rowMeans(.SD, na.rm=T), .SDcols = 3:5]</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">&nbsp; &nbsp;Description &nbsp; &nbsp; &nbsp; ID Anolis_carolinensis Balaena_mysticetus Balaenoptera_acutorostrata_scammoni Sum &nbsp; &nbsp; &nbsp; Avg<br />
+: &nbsp; &nbsp;OG000001 OG000001 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 126 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;103 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 107 336 112.00000<br />
+: &nbsp; &nbsp;OG000002 OG000002 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;70 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 19 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;48 137 &nbsp;45.66667<br />
+: &nbsp; &nbsp;OG000003 OG000003 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;27 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 29 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;25 &nbsp;81 &nbsp;27.00000<br />
+: &nbsp; &nbsp;OG000004 OG000004 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;39 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 36 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;47 122 &nbsp;40.66667<br />
+: &nbsp; &nbsp;OG000005 OG000005 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 1 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 11 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 3 &nbsp;15 &nbsp; 5.00000</span></span></div>

Difference between revisions of "Data.table"

Latest revision as of 12:39, 24 January 2019

Contents

Convert a molten data table into an data table (array type)

Input (head)

Code

Output

Fast melt for Data table

Input (head)

Code

Output (head)

Data table aggregation with 'by'

Input (head)

Code

Output

Data table row-wise calculation

Input (head)

Code

Output

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