Ganti daftar karakter dengan urutan float berdasarkan kerangka data pemetaan
Aug 19 2020
Saya memiliki kerangka data pemetaan dan bingkai data besar di mana setiap baris mewakili protein dengan urutannya.
Saya ingin cara yang efisien untuk memetakan urutan ke nilai yang sesuai dengan asam amino berdasarkan kerangka data pemetaan.
Saya dapat mengulang urutan dan menggantinya dengan kode berikut:
calcStickiness <- function(seq) {
seq_iter <- strsplit(unlist(seq), "")[[1]]
transformed_seq <- c()
for (c in seq_iter) {
transformed_seq <- c(transformed_seq, stickiness_tabel[stickiness_tabel["X"] == c][2])
}
print(transformed_seq)
}
# calling the function
calcStickiness(row["sequence_full"][1])
Dimana stickiness_tabel:
structure(list(X = c("K", "E", "D", "N", "Q", "S", "P", "R",
"T", "H", "A", "G", "M", "V", "L", "I", "F", "C", "Y", "W"),
x = c(-1.25639466063649, -0.928687786101206, -0.700106643211895,
-0.356971499674196, -0.295054350932285, -0.209468209138379,
-0.177787659972006, -0.0892949396458573, 0.0576667944592403,
0.215277407729333, 0.263739398989502, 0.556792734365241,
0.7448899445842, 0.900506232741908, 1.06680680601946, 1.18416532767113,
1.68723510186035, 1.70109173545121, 1.70150269278206, 2.01452547017961
)), class = "data.frame", row.names = c(NA, -20L))
Saya ingin tahu apakah ada cara yang lebih cepat untuk melakukannya karena bingkai data urutan saya memiliki banyak entri di dalamnya.
Baris sederhana dari kerangka data adalah:
structure(list(X = 1L, code = "12as_1", nsub2 = 2L, pdb_error2 = "NO",
QSBIO_err_prob = 3.5, chain_name = "B", sequence_full = "MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILSRVGDGTQDNLSGAEKAVQVKVKALPDAQFEVVHSLAKWKRQTLGQHDFSAGEGLYTHMKALRPDEDRLSPLHSVYVDQWDWERVMGDGERQFSTLKSTVEAIWAGIKATEAAVSEEFGLAPFLPDQIHFVHSQELLSRYPDLDAKGRERAIAKDLGAVFLVGIGGKLSDGHRHDVRAPDYDDWSTPSELGHAGLNGDILVWNPVLEDAFELSSMGIRVDADTLKHQLALTGDEDRLELEWHQALLRGEMPQTIGGGIGQSRLTMLLLQLPHIGQVQAGVWPAAVRESVPSLL"), row.names = 1L, class = "data.frame")
Di mana saya tertarik sequence_full.
Sunting
untuk baris berikut:
MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILSRVGDGTQDNLSGAEKAVQVKVKALPDAQFEVVHSLAKWKRQTLGQHDFSAGEGLYTHMKALRPDEDRLSPLHSVYVDQWDWERVMGDGERQFSTLKSTVEAIWAGIKATEAAVSEEFGLAPFLPDQIHFVHSQELLSRYPDLDAKGRERAIAKDLGAVFLVGIGGKLSDGHRHDVRAPDYDDWSTPSELGHAGLNGDILVWNPVLEDAFELSSMGIRVDADTLKHQLALTGDEDRLELEWHQALLRGEMPQTIGGGIGQSRLTMLLLQLPHIGQVQAGVWPAAVRESVPSLL
Saya ingin mendapatkan sesuatu seperti:
[1] " 0.74488994" "-1.25639466" " 0.05766679" " 0.26373940" " 1.70150269" " 1.18416533" " 0.26373940" "-1.25639466" "-0.29505435"
[10] "-0.08929494" "-0.29505435" " 1.18416533" "-0.20946821" " 1.68723510" " 0.90050623" "-1.25639466" "-0.20946821" " 0.21527741"
[19] " 1.68723510" "-0.20946821" "-0.08929494" "-0.29505435" " 1.06680681" "-0.92868779" "-0.92868779" "-0.08929494" " 1.06680681"
[28] " 0.55679273" " 1.06680681" " 1.18416533" "-0.92868779" " 0.90050623" "-0.29505435" " 0.26373940" "-0.17778766" " 1.18416533"
[37] " 1.06680681" "-0.20946821" "-0.08929494" " 0.90050623" " 0.55679273" "-0.70010664" " 0.55679273" " 0.05766679" "-0.29505435"
[46] "-0.70010664" "-0.35697150" " 1.06680681" "-0.20946821" " 0.55679273" " 0.26373940" "-0.92868779" "-1.25639466" " 0.26373940"
[55] " 0.90050623" "-0.29505435" " 0.90050623" "-1.25639466" " 0.90050623" "-1.25639466" " 0.26373940" " 1.06680681" "-0.17778766"
[64] "-0.70010664" " 0.26373940" "-0.29505435" " 1.68723510" "-0.92868779" " 0.90050623" " 0.90050623" " 0.21527741" "-0.20946821"
[73] " 1.06680681" " 0.26373940" "-1.25639466" " 2.01452547" "-1.25639466" "-0.08929494" "-0.29505435" " 0.05766679" " 1.06680681"
[82] " 0.55679273" "-0.29505435" " 0.21527741" "-0.70010664" " 1.68723510" "-0.20946821" " 0.26373940" " 0.55679273" "-0.92868779"
[91] " 0.55679273" " 1.06680681" " 1.70150269" " 0.05766679" " 0.21527741" " 0.74488994" "-1.25639466" " 0.26373940" " 1.06680681"
[100] "-0.08929494" "-0.17778766" "-0.70010664" "-0.92868779" "-0.70010664" "-0.08929494" " 1.06680681" "-0.20946821" "-0.17778766"
[109] " 1.06680681" " 0.21527741" "-0.20946821" " 0.90050623" " 1.70150269" " 0.90050623" "-0.70010664" "-0.29505435" " 2.01452547"
[118] "-0.70010664" " 2.01452547" "-0.92868779" "-0.08929494" " 0.90050623" " 0.74488994" " 0.55679273" "-0.70010664" " 0.55679273"
[127] "-0.92868779" "-0.08929494" "-0.29505435" " 1.68723510" "-0.20946821" " 0.05766679" " 1.06680681" "-1.25639466" "-0.20946821"
[136] " 0.05766679" " 0.90050623" "-0.92868779" " 0.26373940" " 1.18416533" " 2.01452547" " 0.26373940" " 0.55679273" " 1.18416533"
[145] "-1.25639466" " 0.26373940" " 0.05766679" "-0.92868779" " 0.26373940" " 0.26373940" " 0.90050623" "-0.20946821" "-0.92868779"
[154] "-0.92868779" " 1.68723510" " 0.55679273" " 1.06680681" " 0.26373940" "-0.17778766" " 1.68723510" " 1.06680681" "-0.17778766"
[163] "-0.70010664" "-0.29505435" " 1.18416533" " 0.21527741" " 1.68723510" " 0.90050623" " 0.21527741" "-0.20946821" "-0.29505435"
[172] "-0.92868779" " 1.06680681" " 1.06680681" "-0.20946821" "-0.08929494" " 1.70150269" "-0.17778766" "-0.70010664" " 1.06680681"
[181] "-0.70010664" " 0.26373940" "-1.25639466" " 0.55679273" "-0.08929494" "-0.92868779" "-0.08929494" " 0.26373940" " 1.18416533"
[190] " 0.26373940" "-1.25639466" "-0.70010664" " 1.06680681" " 0.55679273" " 0.26373940" " 0.90050623" " 1.68723510" " 1.06680681"
[199] " 0.90050623" " 0.55679273" " 1.18416533" " 0.55679273" " 0.55679273" "-1.25639466" " 1.06680681" "-0.20946821" "-0.70010664"
[208] " 0.55679273" " 0.21527741" "-0.08929494" " 0.21527741" "-0.70010664" " 0.90050623" "-0.08929494" " 0.26373940" "-0.17778766"
[217] "-0.70010664" " 1.70150269" "-0.70010664" "-0.70010664" " 2.01452547" "-0.20946821" " 0.05766679" "-0.17778766" "-0.20946821"
[226] "-0.92868779" " 1.06680681" " 0.55679273" " 0.21527741" " 0.26373940" " 0.55679273" " 1.06680681" "-0.35697150" " 0.55679273"
[235] "-0.70010664" " 1.18416533" " 1.06680681" " 0.90050623" " 2.01452547" "-0.35697150" "-0.17778766" " 0.90050623" " 1.06680681"
[244] "-0.92868779" "-0.70010664" " 0.26373940" " 1.68723510" "-0.92868779" " 1.06680681" "-0.20946821" "-0.20946821" " 0.74488994"
[253] " 0.55679273" " 1.18416533" "-0.08929494" " 0.90050623" "-0.70010664" " 0.26373940" "-0.70010664" " 0.05766679" " 1.06680681"
[262] "-1.25639466" " 0.21527741" "-0.29505435" " 1.06680681" " 0.26373940" " 1.06680681" " 0.05766679" " 0.55679273" "-0.70010664"
[271] "-0.92868779" "-0.70010664" "-0.08929494" " 1.06680681" "-0.92868779" " 1.06680681" "-0.92868779" " 2.01452547" " 0.21527741"
[280] "-0.29505435" " 0.26373940" " 1.06680681" " 1.06680681" "-0.08929494" " 0.55679273" "-0.92868779" " 0.74488994" "-0.17778766"
[289] "-0.29505435" " 0.05766679" " 1.18416533" " 0.55679273" " 0.55679273" " 0.55679273" " 1.18416533" " 0.55679273" "-0.29505435"
[298] "-0.20946821" "-0.08929494" " 1.06680681" " 0.05766679" " 0.74488994" " 1.06680681" " 1.06680681" " 1.06680681" "-0.29505435"
[307] " 1.06680681" "-0.17778766" " 0.21527741" " 1.18416533" " 0.55679273" "-0.29505435" " 0.90050623" "-0.29505435" " 0.26373940"
[316] " 0.55679273" " 0.90050623" " 2.01452547" "-0.17778766" " 0.26373940" " 0.26373940" " 0.90050623" "-0.08929494" "-0.92868779"
[325] "-0.20946821" " 0.90050623" "-0.17778766" "-0.20946821" " 1.06680681" " 1.06680681"
Outputnya kemudian harus diekspor ke file.
Jawaban
1 Edo Aug 19 2020 at 17:31
Saya memanggil data dengan cara yang sama seperti yang Anda lakukan:
stickiness_tabel <- structure(list(X = c("K", "E", "D", "N", "Q", "S", "P", "R",
"T", "H", "A", "G", "M", "V", "L", "I", "F", "C", "Y", "W"),
x = c(-1.25639466063649, -0.928687786101206, -0.700106643211895,
-0.356971499674196, -0.295054350932285, -0.209468209138379,
-0.177787659972006, -0.0892949396458573, 0.0576667944592403,
0.215277407729333, 0.263739398989502, 0.556792734365241,
0.7448899445842, 0.900506232741908, 1.06680680601946, 1.18416532767113,
1.68723510186035, 1.70109173545121, 1.70150269278206, 2.01452547017961
)), class = "data.frame", row.names = c(NA, -20L))
row <- structure(list(X = 1L, code = "12as_1", nsub2 = 2L, pdb_error2 = "NO",
QSBIO_err_prob = 3.5, chain_name = "B", sequence_full = "MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILSRVGDGTQDNLSGAEKAVQVKVKALPDAQFEVVHSLAKWKRQTLGQHDFSAGEGLYTHMKALRPDEDRLSPLHSVYVDQWDWERVMGDGERQFSTLKSTVEAIWAGIKATEAAVSEEFGLAPFLPDQIHFVHSQELLSRYPDLDAKGRERAIAKDLGAVFLVGIGGKLSDGHRHDVRAPDYDDWSTPSELGHAGLNGDILVWNPVLEDAFELSSMGIRVDADTLKHQLALTGDEDRLELEWHQALLRGEMPQTIGGGIGQSRLTMLLLQLPHIGQVQAGVWPAAVRESVPSLL"), row.names = 1L, class = "data.frame")
Sekarang, yang dapat Anda lakukan adalah ini:
stickiness <- setNames(stickiness_tabel$x, stickiness_tabel$X)
lapply(strsplit(row$sequence_full, split = ""), function(x) stickiness[x])
Ini mengembalikan daftar vektor numerik. Setiap elemen daftar sesuai dengan baris yang Anda ubah, dan setiap vektor adalah vektor bernama tingkat kelekatan yang dinamai dengan huruf yang sesuai.
Apakah ini keluaran yang Anda harapkan? Karena tidak jelas bagi saya dari pertanyaan Anda.
1 Humpelstielzchen Aug 19 2020 at 18:10
Mungkin data.tablesolusi akan sesuai dengan kebutuhan Anda.
Saya membuat kumpulan data sampel 1000 baris dengan mengulangi baris yang Anda berikan.
library(data.table)
df <- row[rep(1, 1000),] #repeat row
df_dt <- setDT(df) # convert to data.table
value <- setNames(stickiness_tabel$x, stickiness_tabel$X)
start <- Sys.time()
df_dt[, sequence_full := lapply(sequence_full, function(x) value[unlist(strsplit(x, split = ""))])]
end <- Sys.time()
end - start
Time difference of 0.03744602 secs
df_dt[1, sequence_full]
[[1]]
M K T A Y I A K Q
0.74488994 -1.25639466 0.05766679 0.26373940 1.70150269 1.18416533 0.26373940 -1.25639466 -0.29505435
R Q I S F V K S H
-0.08929494 -0.29505435 1.18416533 -0.20946821 1.68723510 0.90050623 -1.25639466 -0.20946821 0.21527741
F S R Q L E E R L
1.68723510 -0.20946821 -0.08929494 -0.29505435 1.06680681 -0.92868779 -0.92868779 -0.08929494 1.06680681
G L I E V Q A P I
0.55679273 1.06680681 1.18416533 -0.92868779 0.90050623 -0.29505435 0.26373940 -0.17778766 1.18416533 ...
Ini mengubah tabel lengket Anda menjadi vektor dan mengindeksnya untuk masing-masing sequence_fulldi setiap baris.
Untuk mengeluarkannya, Anda dapat melakukan:
write.csv(stack(unlist(df_dt[1, sequence_full])), file = "~/sequence_output.csv", row.names = F)
Yang mengembalikan csv dengan satu kolom dengan nilai kelekatan dan kolom lainnya dengan elemen urutan.
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