実行手順 (signature) 
¶
ここでは pmsignature を使用した場合のデータの準備方法を解説します。
注釈
実行前にRの環境構築とpmsignatureおよび関連パッケージのインストールが必要です。
インストールおよび、実行コマンドの詳しい解説は pmsignature を参照ください。
別のツールを用いてsignature解析を行った場合は、仕様 に準拠するjsonファイルを別途準備ください。
1. pmsignatureの実行¶
pmsignatureを type="full" で実行してパラメータを出力します。
今回の例では、pmsignatureのサンプルデータを使用しています。
library(pmsignature)
# use sample data
inputFile <- system.file("extdata/Nik_Zainal_2012.mutationPositionFormat.txt.gz", package="pmsignature")
G <- readMPFile(inputFile, numBases = 3, type = "full", trDir = FALSE)
# use background
BG_prob <- readBGFile(G)
Param <- getPMSignature(G, K = 3, BG = BG_prob)
Boot <- bootPMSignature(G, Param0 = Param, bootNum = 100, BG = BG_prob)
# save .Rdata
resultForSave <- list(Param, Boot)
save(resultForSave, file="pmsignature_full3.Rdata")
2. paplotで使用できるように結果ファイルを変換する¶
1で作成した"pmsignature_full3.Rdata" ファイルをpaplotで読み込めるように.json形式に変換します。
変換スクリプトを用意していますので、以下より最新版をダウンロードし、適切な場所に解凍してください。 インストールの必要はありません。
https://github.com/Genomon-Project/genomon_Rscripts/releases
入力ファイル, 出力したいファイル名の順に引数を渡します。
R --vanilla --slave --args ./pmsignature_full3.Rdata ./pmsignature_full3.json < {path to genomon_Rscripts}/pmsignature/convert_toJson_full.R
3. paplotの実行¶
2で作成した"pmsignature_full3.json" ファイルを使用して、paplot を実行します。上述の方法で実行した場合、configファイルの変更は必要ありません。
注釈
backgroundを使用しない場合は、configファイルのbackgroundをFalseに変更してください。
paplot signature pmsignature_full3.Rdata ./temp signature_test
[補足] jsonフォーマット¶
example/signature/Nik_Zainal_2012.full.3.json ファイルをテキストエディタで開くと次のようになっています。
(長いため一部省略しています)
{
"signature":[
[ # signature 1
[0.0018,0.0003,0.0002,0.0005,0.0014,0.0008,0.0002,0.0007,0.0012,0.0003,0.0002,0.0004,0.0271,0.0107,0.0016,0.0145], # C > A
[0.0023,0.0007,0.0001,0.002,0.0027,0.0005,0.0004,0.0032,0.0007,0.0004,0.0001,0.0013,0.1546,0.0306,0.0055,0.1931], # C > G
[0.0043,0.0016,0.0027,0.0019,0.0096,0.0026,0.0046,0.0053,0.0045,0.0021,0.0034,0.0028,0.2612,0.0517,0.0284,0.1335], # C > T
[0.0012,0.0007,0.0004,0.0003,0.0003,0.0003,0,0,0.0003,0.0001,0.0003,0,0.0005,0.0001,0.0001,0.0002], # T > A
[0.0008,0.0003,0.0008,0.0007,0.0002,0.0004,0.0009,0.0005,0.0004,0.0003,0.0006,0.0003,0.0003,0.0004,0.0002,0.0004], # T > C
[0.0001,0.0001,0.0001,0.0001,0,0.0001,0.0001,0,0.0001,0.0001,0.0009,0.0002,0.0001,0,0.0001,0.0005] # T > G
],
[ # signature 2
[0.0266,0.0222,0.0026,0.02,0.0205,0.0145,0.0012,0.0155,0.0155,0.0094,0.0009,0.011,0.0224,0.0177,0.0019,0.0307],
[0.0127,0.0079,0.0035,0.0145,0.0058,0.0048,0.0015,0.0115,0.0034,0.0032,0,0.0071,0.0047,0.0145,0.0006,0.0246],
[0.0232,0.0099,0.042,0.0184,0.014,0.0108,0.0219,0.02,0.0137,0.0102,0.0264,0.0128,0.0048,0.0186,0.0153,0.0165],
[0.0096,0.0084,0.0094,0.0175,0.0075,0.0076,0.0046,0.0123,0.0044,0.0035,0.0028,0.008,0.0176,0.0047,0.0031,0.0139],
[0.0245,0.0087,0.0144,0.0235,0.0098,0.0096,0.0051,0.0102,0.0105,0.0053,0.0042,0.0108,0.0114,0.0081,0.0038,0.0098],
[0.0046,0.0006,0.0036,0.0035,0.0025,0.0009,0.0028,0.0082,0.0023,0.0005,0.004,0.0048,0.0041,0.0012,0.0056,0.0104]
]
],
"id":["PD3851a","PD3890a","PD3904a"],
"mutation":[[0,0,0.0594],[0,1,0.7677],[0,2,0.1727],[1,0,0.1474],[1,1,0.4064],[1,2,0.4461]],
"mutation_count":[4001,7174,5804]
}
signature描画データ
| signature: | signatureの各barの値。
signatureごと、変化パターン (C > A など) ごとに値を記述します。
変化パターンの数を変えることはできません。
baseの数は3か5のいずれかのみ設定できます。
|
|---|
今回の例ではbase=3のため次の順に16ケースの値を記述します。(R=Reference)
ARA,ARC,ARG,ART,CRA,CRA,CRG,CRT,GRA,GRC,GRG,GRT,TRA,TRA,TRG,TRT
もしbase=5とする場合は、次の順に256ケースの記述が必要です。(R=Reference)
AARAA,AARAC,AARAG,AARAT,AARCA,AARCC,AARCG,AARCT,AARGA,AARGC,AARGG,AARGT,AARTA,AARTC,AARTG,AARTT,
ACRAA,ACRAC,ACRAG,ACRAT,ACRCA,ACRCC,ACRCG,ACRCT,ACRGA,ACRGC,ACRGG,ACRGT,ACRTA,ACRTC,ACRTG,ACRTT,
AGRAA,AGRAC,AGRAG,AGRAT,AGRCA,AGRCC,AGRCG,AGRCT,AGRGA,AGRGC,AGRGG,AGRGT,AGRTA,AGRTC,AGRTG,AGRTT,
ATRAA,ATRAC,ATRAG,ATRAT,ATRCA,ATRCC,ATRCG,ATRCT,ATRGA,ATRGC,ATRGG,ATRGT,ATRTA,ATRTC,ATRTG,ATRTT,
CARAA,CARAC,CARAG,CARAT,CARCA,CARCC,CARCG,CARCT,CARGA,CARGC,CARGG,CARGT,CARTA,CARTC,CARTG,CARTT,
CCRAA,CCRAC,CCRAG,CCRAT,CCRCA,CCRCC,CCRCG,CCRCT,CCRGA,CCRGC,CCRGG,CCRGT,CCRTA,CCRTC,CCRTG,CCRTT,
CGRAA,CGRAC,CGRAG,CGRAT,CGRCA,CGRCC,CGRCG,CGRCT,CGRGA,CGRGC,CGRGG,CGRGT,CGRTA,CGRTC,CGRTG,CGRTT,
CTRAA,CTRAC,CTRAG,CTRAT,CTRCA,CTRCC,CTRCG,CTRCT,CTRGA,CTRGC,CTRGG,CTRGT,CTRTA,CTRTC,CTRTG,CTRTT,
GARAA,GARAC,GARAG,GARAT,GARCA,GARCC,GARCG,GARCT,GARGA,GARGC,GARGG,GARGT,GARTA,GARTC,GARTG,GARTT,
GCRAA,GCRAC,GCRAG,GCRAT,GCRCA,GCRCC,GCRCG,GCRCT,GCRGA,GCRGC,GCRGG,GCRGT,GCRTA,GCRTC,GCRTG,GCRTT,
GGRAA,GGRAC,GGRAG,GGRAT,GGRCA,GGRCC,GGRCG,GGRCT,GGRGA,GGRGC,GGRGG,GGRGT,GGRTA,GGRTC,GGRTG,GGRTT,
GTRAA,GTRAC,GTRAG,GTRAT,GTRCA,GTRCC,GTRCG,GTRCT,GTRGA,GTRGC,GTRGG,GTRGT,GTRTA,GTRTC,GTRTG,GTRTT,
TARAA,TARAC,TARAG,TARAT,TARCA,TARCC,TARCG,TARCT,TARGA,TARGC,TARGG,TARGT,TARTA,TARTC,TARTG,TARTT,
TCRAA,TCRAC,TCRAG,TCRAT,TCRCA,TCRCC,TCRCG,TCRCT,TCRGA,TCRGC,TCRGG,TCRGT,TCRTA,TCRTC,TCRTG,TCRTT,
TGRAA,TGRAC,TGRAG,TGRAT,TGRCA,TGRCC,TGRCG,TGRCT,TGRGA,TGRGC,TGRGG,TGRGT,TGRTA,TGRTC,TGRTG,TGRTT,
TTRAA,TTRAC,TTRAG,TTRAT,TTRCA,TTRCC,TTRCG,TTRCT,TTRGA,TTRGC,TTRGG,TTRGT,TTRTA,TTRTC,TTRTG,TTRTT
積み上げグラフ描画データ
| id: | サンプル名リスト
|
|---|---|
| mutation_count: | サンプルごとのmutation数
上記の例の場合、PD3851a のmutation数=4001, PD3890a のmutation数=7174, PD3904a のmutation数=5804 となります。
|
| mutation: | サンプルごと、signatureごとの割合を設定します。
[sample index, signature index, value] の順に記載します。
サンプルのindexは id で記載した順に0からカウントします。
上記の例の場合、PD3851a=0, PD3890a=1, PD3904a=2となります。
signatureのindexも ref で記載した順に0からカウントします。
backgroundを使用する場合、signature1, signature2, ..., backgroundの順にカウントします。
上記の例の場合、signature1 = 0, signature2 = 1, background = 2となります。
|
注釈
key名は変更可能です。key名を変更した場合は設定ファイル ([result_format_signature] key_*)を変更してください。
注釈
jsonとしての形式の厳密さについては、paplotはpythonのjsonパッケージを使用しているため、次のコマンドで読めればOKです。
python jsonパッケージを使用したファイル確認例 (ファイル名が "Nik_Zainal_2012.full.3.json" の場合)
$ python
>>> import json
>>> json.load(open("Nik_Zainal_2012.full.3.json"))