5
おそらく、この問題の解決方法は非常に簡単ですが、私はグーグルで見つけられませんでした。またはdata.table FAQです。あなたが見ることができるように、行の多くの値が列の一部について、繰り返している最小条件を使用したサブセットdata.table
> test
chr bp ID REF ALT AF AC AN EFFECT IMPACT FUNCLASS CODING GENE pos effRank
1: 1 860416 rs61464428 G A 0.5000000 14 28 UPSTREAM MODIFIER CODING SAMD11 1:860416 21
2: 1 860416 rs61464428 G A 0.5000000 14 28 UPSTREAM MODIFIER CODING SAMD11 1:860416 21
3: 1 860416 rs61464428 G A 0.5000000 14 28 DOWNSTREAM MODIFIER CODING AL645608.1 1:860416 22
4: 1 860461 rs57465118 G A 1.0000000 62 62 UPSTREAM MODIFIER CODING SAMD11 1:860461 21
5: 1 860461 rs57465118 G A 1.0000000 62 62 UPSTREAM MODIFIER CODING SAMD11 1:860461 21
6: 1 860461 rs57465118 G A 1.0000000 62 62 DOWNSTREAM MODIFIER CODING AL645608.1 1:860461 22
7: 1 860521 rs57924093 C A 0.9840000 61 62 UPSTREAM MODIFIER CODING SAMD11 1:860521 21
8: 1 860521 rs57924093 C A 0.9840000 61 62 UPSTREAM MODIFIER CODING SAMD11 1:860521 21
9: 1 860521 rs57924093 C A 0.9840000 61 62 DOWNSTREAM MODIFIER CODING AL645608.1 1:860521 22
10: 1 861261 rs144896029 G A 0.0027270 3 1100 UPSTREAM MODIFIER CODING SAMD11 1:861261 21
11: 1 861261 rs144896029 G A 0.0027270 3 1100 DOWNSTREAM MODIFIER CODING AL645608.1 1:861261 22
12: 1 861332 G A 0.0009074 1 1102 NON_SYNONYMOUS_CODING MODERATE MISSENSE CODING AL645608.1 1:861332 11
13: 1 861332 G A 0.0009074 1 1102 NON_SYNONYMOUS_CODING MODERATE MISSENSE CODING SAMD11 1:861332 11
14: 1 861332 G A 0.0009074 1 1102 NON_SYNONYMOUS_CODING MODERATE MISSENSE CODING SAMD11 1:861332 11
15: 1 861332 G A 0.0009074 1 1102 NON_SYNONYMOUS_CODING MODERATE MISSENSE CODING SAMD11 1:861332 11
16: 1 861332 G A 0.0009074 1 1102 UPSTREAM MODIFIER CODING SAMD11 1:861332 21
17: 1 865455 C G 0.0033190 3 904 UPSTREAM MODIFIER CODING SAMD11 1:865455 21
18: 1 865628 rs41285790 G A 0.0027780 3 1080 NON_SYNONYMOUS_CODING MODERATE MISSENSE CODING SAMD11 1:865628 11
19: 1 865628 rs41285790 G A 0.0027780 3 1080 NON_SYNONYMOUS_CODING MODERATE MISSENSE CODING SAMD11 1:865628 11
20: 1 865628 rs41285790 G A 0.0027780 3 1080 NON_SYNONYMOUS_CODING MODERATE MISSENSE CODING SAMD11 1:865628 11
21: 1 865628 rs41285790 G A 0.0027780 3 1080 SYNONYMOUS_CODING LOW SILENT CODING AL645608.1 1:865628 14
22: 1 865628 rs41285790 G A 0.0027780 3 1080 UPSTREAM MODIFIER CODING SAMD11 1:865628 21
23: 1 866437 rs139076934 C T 0.0009074 1 1102 SYNONYMOUS_CODING LOW SILENT CODING AL645608.1 1:866437 14
24: 1 866437 rs139076934 C T 0.0009074 1 1102 SYNONYMOUS_CODING LOW SILENT CODING SAMD11 1:866437 14
25: 1 866437 rs139076934 C T 0.0009074 1 1102 SYNONYMOUS_CODING LOW SILENT CODING SAMD11 1:866437 14
26: 1 866437 rs139076934 C T 0.0009074 1 1102 SYNONYMOUS_CODING LOW SILENT CODING SAMD11 1:866437 14
27: 1 866461 rs148884928 G A 0.0009074 1 1102 SYNONYMOUS_CODING LOW SILENT CODING SAMD11 1:866461 14
28: 1 866461 rs148884928 G A 0.0009074 1 1102 SYNONYMOUS_CODING LOW SILENT CODING SAMD11 1:866461 14
29: 1 866461 rs148884928 G A 0.0009074 1 1102 SYNONYMOUS_CODING LOW SILENT CODING SAMD11 1:866461 14
30: 1 866461 rs148884928 G A 0.0009074 1 1102 UPSTREAM MODIFIER CODING AL645608.1 1:866461 21
31: 1 866511 rs71576583 CCCCT CCCCTCCCT 1.0000000 148 148 UPSTREAM MODIFIER CODING AL645608.1 1:866511 21
32: 1 871057 C T 0.0009074 1 1102 UPSTREAM MODIFIER CODING SAMD11 1:871057 21
33: 1 871057 C T 0.0009074 1 1102 UPSTREAM MODIFIER CODING AL645608.1 1:871057 21
34: 1 871057 C T 0.0009074 1 1102 UPSTREAM MODIFIER CODING SAMD11 1:871057 21
35: 1 871215 rs28419423 C G 0.0036300 4 1102 SYNONYMOUS_CODING LOW SILENT CODING SAMD11 1:871215 14
36: 1 871215 rs28419423 C G 0.0036300 4 1102 SYNONYMOUS_CODING LOW SILENT CODING SAMD11 1:871215 14
37: 1 871215 rs28419423 C G 0.0036300 4 1102 UPSTREAM MODIFIER CODING SAMD11 1:871215 21
38: 1 871215 rs28419423 C G 0.0036300 4 1102 UPSTREAM MODIFIER CODING SAMD11 1:871215 21
39: 1 871215 rs28419423 C G 0.0036300 4 1102 UPSTREAM MODIFIER CODING AL645608.1 1:871215 21
40: 1 871215 rs28419423 C G 0.0036300 4 1102 DOWNSTREAM MODIFIER CODING SAMD11 1:871215 22
41: 1 871287 C G 0.0009107 1 1098 UPSTREAM MODIFIER CODING SAMD11 1:871287 21
42: 1 871287 C G 0.0009107 1 1098 UPSTREAM MODIFIER CODING SAMD11 1:871287 21
43: 1 871287 C G 0.0009107 1 1098 UPSTREAM MODIFIER CODING AL645608.1 1:871287 21
44: 1 871287 C G 0.0009107 1 1098 DOWNSTREAM MODIFIER CODING SAMD11 1:871287 22
45: 1 871334 rs4072383 G T 0.6680000 474 710 UPSTREAM MODIFIER CODING SAMD11 1:871334 21
46: 1 871334 rs4072383 G T 0.6680000 474 710 UPSTREAM MODIFIER CODING SAMD11 1:871334 21
47: 1 871334 rs4072383 G T 0.6680000 474 710 UPSTREAM MODIFIER CODING AL645608.1 1:871334 21
48: 1 871334 rs4072383 G T 0.6680000 474 710 DOWNSTREAM MODIFIER CODING SAMD11 1:871334 22
49: 1 874415 rs74047412 C T 0.0018250 2 1096 UPSTREAM MODIFIER CODING SAMD11 1:874415 21
50: 1 874415 rs74047412 C T 0.0018250 2 1096 UPSTREAM MODIFIER CODING SAMD11 1:874415 21
chr bp ID REF ALT AF AC AN EFFECT IMPACT FUNCLASS CODING GENE pos effRank
：
私はdata.tableとても似ています。私がしたいのは、effRank変数の値（最小値）に基づいて、重複した行を削除することです。キーをchr,bp、effRankに設定しました。したがって、これらの3つの列に基づいて表をソートする必要があります。私は一種の近づいた。次のコマンドは、必要な行を返しますが、必要なすべての列を返しません。
> test[,min(effRank), by=pos]
pos V1
1: 1:860416 21
2: 1:860461 21
3: 1:860521 21
4: 1:861261 21
5: 1:861332 11
6: 1:865455 21
7: 1:865628 11
8: 1:866437 14
9: 1:866461 14
10: 1:866511 21
11: 1:871057 21
12: 1:871215 14
13: 1:871287 21
14: 1:871334 21
15: 1:874415 21
私は必要なのは、上記のコマンドは、式の中で言及さdata.tableだけでなく、もののすべての列を返すようにする方法です。それ以外の場合は、完全に動作します。どんな助けもありがとうございます。 dputの出力は以下のとおりです。
乾杯、 デイビー
> dput(test)
structure(list(chr = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), bp = c(860416L, 860416L, 860416L,
860461L, 860461L, 860461L, 860521L, 860521L, 860521L, 861261L,
861261L, 861332L, 861332L, 861332L, 861332L, 861332L, 865455L,
865628L, 865628L, 865628L, 865628L, 865628L, 866437L, 866437L,
866437L, 866437L, 866461L, 866461L, 866461L, 866461L, 866511L,
871057L, 871057L, 871057L, 871215L, 871215L, 871215L, 871215L,
871215L, 871215L, 871287L, 871287L, 871287L, 871287L, 871334L,
871334L, 871334L, 871334L, 874415L, 874415L), ID = structure(c(10L,
10L, 10L, 8L, 8L, 8L, 9L, 9L, 9L, 3L, 3L, 1L, 1L, 1L, 1L, 1L,
1L, 7L, 7L, 7L, 7L, 7L, 2L, 2L, 2L, 2L, 4L, 4L, 4L, 4L, 11L,
1L, 1L, 1L, 5L, 5L, 5L, 5L, 5L, 5L, 1L, 1L, 1L, 1L, 6L, 6L, 6L,
6L, 12L, 12L), .Label = c("", "rs139076934", "rs144896029", "rs148884928",
"rs28419423", "rs4072383", "rs41285790", "rs57465118", "rs57924093",
"rs61464428", "rs71576583", "rs74047412"), class = "factor"),
REF = structure(c(3L, 3L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 1L, 3L, 3L, 3L, 3L, 3L, 1L, 1L, 1L,
1L, 3L, 3L, 3L, 3L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 3L, 3L, 3L, 3L, 1L, 1L), .Label = c("C",
"CCCCT", "G"), class = "factor"), ALT = structure(c(1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 3L,
1L, 1L, 1L, 1L, 1L, 4L, 4L, 4L, 4L, 1L, 1L, 1L, 1L, 2L, 4L,
4L, 4L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L,
4L, 4L, 4L), .Label = c("A", "CCCCTCCCT", "G", "T"), class = "factor"),
AF = c(0.5, 0.5, 0.5, 1, 1, 1, 0.984, 0.984, 0.984, 0.002727,
0.002727, 0.0009074, 0.0009074, 0.0009074, 0.0009074, 0.0009074,
0.003319, 0.002778, 0.002778, 0.002778, 0.002778, 0.002778,
0.0009074, 0.0009074, 0.0009074, 0.0009074, 0.0009074, 0.0009074,
0.0009074, 0.0009074, 1, 0.0009074, 0.0009074, 0.0009074,
0.00363, 0.00363, 0.00363, 0.00363, 0.00363, 0.00363, 0.0009107,
0.0009107, 0.0009107, 0.0009107, 0.668, 0.668, 0.668, 0.668,
0.001825, 0.001825), AC = c(14L, 14L, 14L, 62L, 62L, 62L,
61L, 61L, 61L, 3L, 3L, 1L, 1L, 1L, 1L, 1L, 3L, 3L, 3L, 3L,
3L, 3L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 148L, 1L, 1L, 1L,
4L, 4L, 4L, 4L, 4L, 4L, 1L, 1L, 1L, 1L, 474L, 474L, 474L,
474L, 2L, 2L), AN = c(28L, 28L, 28L, 62L, 62L, 62L, 62L,
62L, 62L, 1100L, 1100L, 1102L, 1102L, 1102L, 1102L, 1102L,
904L, 1080L, 1080L, 1080L, 1080L, 1080L, 1102L, 1102L, 1102L,
1102L, 1102L, 1102L, 1102L, 1102L, 148L, 1102L, 1102L, 1102L,
1102L, 1102L, 1102L, 1102L, 1102L, 1102L, 1098L, 1098L, 1098L,
1098L, 710L, 710L, 710L, 710L, 1096L, 1096L), EFFECT = structure(c(4L,
4L, 1L, 4L, 4L, 1L, 4L, 4L, 1L, 4L, 1L, 2L, 2L, 2L, 2L, 4L,
4L, 2L, 2L, 2L, 3L, 4L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L,
4L, 4L, 4L, 3L, 3L, 4L, 4L, 4L, 1L, 4L, 4L, 4L, 1L, 4L, 4L,
4L, 1L, 4L, 4L), .Label = c("DOWNSTREAM", "NON_SYNONYMOUS_CODING",
"SYNONYMOUS_CODING", "UPSTREAM"), class = "factor"), IMPACT = structure(c(3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 2L, 2L, 2L, 2L, 3L,
3L, 2L, 2L, 2L, 1L, 3L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 3L, 3L,
3L, 3L, 3L, 1L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L), .Label = c("LOW", "MODERATE", "MODIFIER"
), class = "factor"), FUNCLASS = structure(c(1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 1L, 2L,
2L, 2L, 3L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 1L,
1L, 3L, 3L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L), .Label = c("", "MISSENSE", "SILENT"), class = "factor"),
CODING = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), .Label = "CODING", class = "factor"),
GENE = structure(c(2L, 2L, 1L, 2L, 2L, 1L, 2L, 2L, 1L, 2L,
1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 2L, 2L,
2L, 2L, 2L, 2L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 2L,
2L, 2L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 2L), .Label = c("AL645608.1",
"SAMD11"), class = "factor"), pos = structure(c(1L, 1L, 1L,
2L, 2L, 2L, 3L, 3L, 3L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 6L, 7L,
7L, 7L, 7L, 7L, 8L, 8L, 8L, 8L, 9L, 9L, 9L, 9L, 10L, 11L,
11L, 11L, 12L, 12L, 12L, 12L, 12L, 12L, 13L, 13L, 13L, 13L,
14L, 14L, 14L, 14L, 15L, 15L), .Label = c("1:860416", "1:860461",
"1:860521", "1:861261", "1:861332", "1:865455", "1:865628",
"1:866437", "1:866461", "1:866511", "1:871057", "1:871215",
"1:871287", "1:871334", "1:874415"), class = "factor"), effRank = c(21L,
21L, 22L, 21L, 21L, 22L, 21L, 21L, 22L, 21L, 22L, 11L, 11L,
11L, 11L, 21L, 21L, 11L, 11L, 11L, 14L, 21L, 14L, 14L, 14L,
14L, 14L, 14L, 14L, 21L, 21L, 21L, 21L, 21L, 14L, 14L, 21L,
21L, 21L, 22L, 21L, 21L, 21L, 22L, 21L, 21L, 21L, 22L, 21L,
21L)), .Names = c("chr", "bp", "ID", "REF", "ALT", "AF",
"AC", "AN", "EFFECT", "IMPACT", "FUNCLASS", "CODING", "GENE",
"pos", "effRank"), row.names = c(NA, -50L), class = c("data.table",
"data.frame"), .internal.selfref = <pointer: 0x0000000004260788>, sorted = c("chr",
"bp", "effRank"))
優秀！ありがとうございました。私はドキュメンテーションでそれを完全に見逃しましたか？ –