Настройка четности переполнения стека защиты R (выражения = 5e5): невозможно разделить кадр данных - PullRequest
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Настройка четности переполнения стека защиты R (выражения = 5e5): невозможно разделить кадр данных

0 голосов
/ 22 февраля 2020

Я выполняю анализ экспрессии гена в R и, следовательно, работаю с большим количеством данных. Я хочу применить модель Кокса к этим данным (249R на 23000 C), но когда я пытаюсь это сделать, я получаю сообщение об ошибке (Protect (): переполнение стека защиты). Я понимаю, что многие другие задавали этот вопрос, и я пытался использовать ответы на эти предыдущие вопросы, такие как параметры (выражения = 5e5), а также gl mnet, но последний дает мне ошибку (Ошибка в [.data.frame (data, c (lhsVars, rhsVars)): выбраны неопределенные столбцы), и я не уверен, как его использовать при выполнении регрессии Кокса, и предыдущая опция не работает. Кроме того, учитывая то, как я работаю над своим проектом, я не могу разделить мой фрейм данных.

Я приложил свой код и был бы очень признателен за любую помощь! Извините, если мой код запутан - я студент, и мне еще многое предстоит узнать. 

totranspose <- read.delim("/Users/menon/OneDrive/Desktop/csrsef files/FilesToTranspose.txt", stringsAsFactors = F, header = T)
rownames(totranspose) <- totranspose$X
totranspose$X <- NULL
finaldatacsrsef <- t(totranspose)
colnames(finaldatacsrsef) <- as.character(unlist(finaldatacsrsef[1,]))
finaldatacsrsef <- finaldatacsrsef[-1,]

library(survival)
initData <- data.frame(finaldatacsrsef)
eventfreetime <- initData[ , c("EFST")] 
vitalstatus <- initData[ , c("Status")]
temporaryObj <- Surv(as.numeric(eventfreetime), vitalstatus == 2)
finalDataa <- data.frame(SurvObj = temporaryObj)
finalDataa <- cbind(finalDataa, initData[, 3:ncol(initData)])
options(expressions = 5e5)
finalcox <- coxph(SurvObj ~ ., data =  finalDataa)
summary(finalcox)$coefficients

Спасибо!

Редактировать: Вот как выглядят мои данные (имена пациентов являются заголовками строк, имена генов являются заголовками столбцов) 

> dput(initData[1:10, 1:10])
structure(list(EFST = structure(c(TARGET.30.PAAPFA = 166L, TARGET.30.PACLJN = 193L, 
TARGET.30.PACRYY = 189L, TARGET.30.PACRZM = 233L, TARGET.30.PACSNL = 45L, 
TARGET.30.PACSSR = 176L, TARGET.30.PACUGP = 141L, TARGET.30.PACVNB = 63L, 
TARGET.30.PACYGY = 75L, TARGET.30.PACZPX = 194L), .Label = c(" 2.00000", 
" 9.00000", "1002.00000", "1013.00000", "1022.00000", "1030.00000", 
...
"165.00000", "1659.00000", "168.00000", "1696.00000", "1707.00000", 
"1710.00000", "172.00000", "1749.00000", "1795.00000", "1836.00000", 
"1843.00000", "1880.00000", "190.00000", "1933.00000", "1964.00000", 
"2007.00000", "2025.00000", "203.00000", "205.00000", "206.00000", 
"2147.00000", "2155.00000", "217.00000", "2183.00000", "219.00000", 
...
"887.00000", "922.00000", "932.00000", "956.00000", "964.00000", 
"968.00000"), class = "factor"), Status = structure(c(TARGET.30.PAAPFA = 4L, 
TARGET.30.PACLJN = 1L, TARGET.30.PACRYY = 1L, TARGET.30.PACRZM = 4L, 
TARGET.30.PACSNL = 4L, TARGET.30.PACSSR = 7L, TARGET.30.PACUGP = 4L, 
TARGET.30.PACVNB = 4L, TARGET.30.PACYGY = 4L, TARGET.30.PACZPX = 1L
), .Label = c("   1.00000", "   2.00000", "  1.00000", "  2.00000", 
"  2.000000", " 1.00000", " 2.00000"), class = "factor"), AADACL3 = structure(c(TARGET.30.PAAPFA = 219L, 
TARGET.30.PACLJN = 103L, TARGET.30.PACRYY = 83L, TARGET.30.PACRZM = 234L, 
TARGET.30.PACSNL = 150L, TARGET.30.PACSSR = 247L, TARGET.30.PACUGP = 140L, 
TARGET.30.PACVNB = 118L, TARGET.30.PACYGY = 227L, TARGET.30.PACZPX = 99L
), .Label = c("   4.70471", "   4.71884", "   4.75278", "   4.77252", 
"   4.79924", "   4.82726", "   4.83177", "   4.85297", "   4.85348", 
...
"  5.74958", "  5.76020", "  5.77283", "  5.77490", "  5.79089", 
"  5.91416", " 5.02643", " 5.16070", " 5.20377", " 5.33849", 
" 5.43057", " 5.70252", " 5.88764"), class = "factor"), AADACL4 = structure(c(TARGET.30.PAAPFA = 201L, 
TARGET.30.PACLJN = 104L, TARGET.30.PACRYY = 75L, TARGET.30.PACRZM = 213L, 
TARGET.30.PACSNL = 112L, TARGET.30.PACSSR = 247L, TARGET.30.PACUGP = 170L, 
TARGET.30.PACVNB = 199L, TARGET.30.PACYGY = 140L, TARGET.30.PACZPX = 30L
), .Label = c("   4.37049", "   4.41956", "   4.56399", "   4.60298", 
"   4.66085", "   4.66949", "   4.67545", "   4.69108", "   4.69205", 
...
"  5.77346", " 4.84060", " 4.93969", " 5.01135", " 5.03256", 
" 5.22472", " 5.29179", " 5.70923"), class = "factor"), ACADM = structure(c(TARGET.30.PAAPFA = 182L, 
TARGET.30.PACLJN = 37L, TARGET.30.PACRYY = 86L, TARGET.30.PACRZM = 218L, 
TARGET.30.PACSNL = 238L, TARGET.30.PACSSR = 241L, TARGET.30.PACUGP = 215L, 
TARGET.30.PACVNB = 201L, TARGET.30.PACYGY = 131L, TARGET.30.PACZPX = 70L
), .Label = c("   6.25757", "   6.33278", "   6.39292", "   6.61567", 
"   6.70676", "   6.77349", "   6.82724", "   6.84948", "   6.88238", 
"   7.03772", "   7.08124", "   7.11364", "   7.16697", "   7.21509", 
"   7.21749", "   7.22232", "   7.22508", "   7.24340", "   7.26963", 
"   7.27326", "   7.28288", "   7.29225", "   7.30015", "   7.31206", 
….
" 7.94490", " 8.10245", " 8.15717"), class = "factor"), ACOT11 = structure(c(TARGET.30.PAAPFA = 211L, 
TARGET.30.PACLJN = 25L, TARGET.30.PACRYY = 35L, TARGET.30.PACRZM = 176L, 
TARGET.30.PACSNL = 196L, TARGET.30.PACSSR = 247L, TARGET.30.PACUGP = 156L, 
TARGET.30.PACVNB = 186L, TARGET.30.PACYGY = 199L, TARGET.30.PACZPX = 63L
), .Label = c("   5.93635", "   5.94244", "   5.95103", "   5.98901", 
"   6.03946", "   6.11429", "   6.11859", "   6.13903", "   6.15869", 
 ...
" 6.54330", " 6.58306", " 6.78981"), class = "factor"), ACOT7 = structure(c(TARGET.30.PAAPFA = 177L, 
TARGET.30.PACLJN = 88L, TARGET.30.PACRYY = 15L, TARGET.30.PACRZM = 227L, 
TARGET.30.PACSNL = 176L, TARGET.30.PACSSR = 243L, TARGET.30.PACUGP = 112L, 
TARGET.30.PACVNB = 234L, TARGET.30.PACYGY = 190L, TARGET.30.PACZPX = 2L
), .Label = c("   7.27372", "   7.44455", "   7.57713", "   7.63049", 
"   7.67607", "   7.67940", "   7.67984", "   7.69863", "   7.74928", 
"   7.79042", "   7.79045", "   7.79654", "   7.81007", "   7.83489", 
"   7.83490", "   7.83660", "   7.85289", "   7.86943", "   7.87172", 
"   7.87769", "   7.88242", "   7.89099", "   7.91394", "   7.91521", 
"   7.91740", "   7.93080", "   7.93191", "   7.94568", "   7.96315", 
"   7.97490", "   7.98972", "   7.99591", "   8.00916", "   8.01633", 
"   8.02621", "   8.03156", "   8.03209", "   8.04701", "   8.05113", 
"   8.05589", "   8.05917", "   8.06400", "   8.06733", "   8.08233", 
"   8.10082", "   8.10544", "   8.11094", "   8.12160", "   8.13253", 
"   8.13579", "   8.14512", "   8.14566", "   8.15169", "   8.15522", 
"   8.15733", "   8.16079", "   8.16116", "   8.16126", "   8.16969", 
"   8.17116", "   8.18370", "   8.20090", "   8.20675", "   8.20713", 
"   8.21006", "   8.21736", "   8.21749", "   8.21878", "   8.24505", 
"   8.24802", "   8.25781", "   8.27362", "   8.27436", "   8.27646", 
"   8.28431", "   8.28967", "   8.29238", "   8.29331", "   8.29626", 
"   8.31274", "   8.31330", "   8.31784", "   8.31881", "   8.32197", 
"   8.34618", "   8.35837", "   8.37840", "   8.38011", "   8.38226", 
"   8.38984", "   8.40466", "   8.44161", "   8.45682", "   8.46116", 
"   8.49594", "   8.50602", "   8.52247", "   8.53077", "   8.55986", 
"   8.57609", "   8.70593", "   8.78929", "   8.79241", "   8.83021", 
"   8.88021", "   8.89001", "   8.90448", "   9.11322", "   9.43475", 
"  7.52861", "  7.66466", "  7.68660", "  7.70969", "  7.71580", 
"  7.72014", "  7.73900", "  7.73927", "  7.74026", "  7.75380", 
"  7.75922", "  7.76969", "  7.77150", "  7.78116", "  7.78417", 
"  7.79180", "  7.79952", "  7.80261", "  7.80837", "  7.81161", 
"  7.81396", "  7.82174", "  7.82495", "  7.82584", "  7.82670", 
"  7.83582", "  7.83650", "  7.85396", "  7.85827", "  7.87575", 
"  7.88243", "  7.88348", "  7.88520", "  7.88999", "  7.90379", 
"  7.91414", "  7.91715", "  7.93460", "  7.93812", "  7.96672", 
"  7.97637", "  7.98229", "  7.98352", "  8.00525", "  8.01628", 
"  8.01696", "  8.01744", "  8.01888", "  8.01977", "  8.02221", 
"  8.02997", "  8.03639", "  8.04479", "  8.05963", "  8.07101", 
"  8.07438", "  8.07717", "  8.08261", "  8.08476", "  8.09201", 
"  8.09559", "  8.10024", "  8.10100", "  8.10383", "  8.10417", 
"  8.11497", "  8.11502", "  8.11807", "  8.12097", "  8.12552", 
"  8.13045", "  8.13261", "  8.13270", "  8.13377", "  8.13397", 
"  8.13897", "  8.14309", "  8.14993", "  8.15376", "  8.15771", 
"  8.17004", "  8.17409", "  8.17599", "  8.19405", "  8.20733", 
"  8.21219", "  8.22061", "  8.23543", "  8.23934", "  8.24026", 
"  8.24202", "  8.24563", "  8.26212", "  8.26387", "  8.26394", 
"  8.27844", "  8.27997", "  8.29101", "  8.30884", "  8.31898", 
"  8.32005", "  8.32071", "  8.32172", "  8.32829", "  8.32889", 
"  8.33430", "  8.33625", "  8.34192", "  8.34423", "  8.36700", 
"  8.37298", "  8.37877", "  8.39039", "  8.41815", "  8.42202", 
"  8.42291", "  8.43199", "  8.43645", "  8.43953", "  8.48244", 
"  8.49337", "  8.49969", "  8.52678", "  8.54624", "  8.55327", 
"  8.57020", "  8.57290", "  8.66956", "  8.67772", "  8.78580", 
"  9.096890", " 7.80377", " 7.84975", " 8.01090", " 8.18525", 
" 8.22819", " 8.25531", " 8.47783"), class = "factor"), ACTB = structure(c(TARGET.30.PAAPFA = 139L, 
TARGET.30.PACLJN = 93L, TARGET.30.PACRYY = 90L, TARGET.30.PACRZM = 218L, 
TARGET.30.PACSNL = 164L, TARGET.30.PACSSR = 237L, TARGET.30.PACUGP = 211L, 
TARGET.30.PACVNB = 230L, TARGET.30.PACYGY = 202L, TARGET.30.PACZPX = 37L
), .Label = c("  10.29300", "  10.33920", "  10.37040", "  10.51230", 
"  10.52510", "  10.55200", "  10.57640", "  10.60880", "  10.63620", 

"10.84560", "10.85970", "11.00500", "11.11320"), class = "factor"), 
    ACTL8 = structure(c(TARGET.30.PAAPFA = 212L, TARGET.30.PACLJN = 73L, 
    TARGET.30.PACRYY = 24L, TARGET.30.PACRZM = 196L, TARGET.30.PACSNL = 151L, 
    TARGET.30.PACSSR = 247L, TARGET.30.PACUGP = 148L, TARGET.30.PACVNB = 124L, 
    TARGET.30.PACYGY = 236L, TARGET.30.PACZPX = 61L), .Label = c("   5.24716", 
    "   5.37788", "   5.46886", "   5.52772", "   5.56753", "   5.57768", 
    ...
    " 6.69476"), class = "factor")), row.names = c("TARGET.30.PAAPFA", 
"TARGET.30.PACLJN", "TARGET.30.PACRYY", "TARGET.30.PACRZM", "TARGET.30.PACSNL", 
"TARGET.30.PACSSR", "TARGET.30.PACUGP", "TARGET.30.PACVNB", "TARGET.30.PACYGY", 
"TARGET.30.PACZPX"), class = "data.frame")
...