{"id":26112,"date":"2024-01-24T17:18:47","date_gmt":"2024-01-24T09:18:47","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=26112"},"modified":"2024-01-24T17:18:48","modified_gmt":"2024-01-24T09:18:48","slug":"r%e8%af%ad%e8%a8%80%e5%8c%85generics%e6%95%99%e4%bd%a0%e5%bf%ab%e9%80%9f%e9%80%9a%e8%bf%87%e5%87%bd%e6%95%b0%e7%ae%80%e5%8c%96%e5%b9%b6%e5%a4%84%e7%90%86%e7%94%9f%e7%89%a9%e5%ad%a6%e6%95%b0%e6%8d%ae","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=26112","title":{"rendered":"R\u8bed\u8a00\u5305generics\u6559\u4f60\u5feb\u901f\u901a\u8fc7\u51fd\u6570\u7b80\u5316\u5e76\u5904\u7406\u751f\u7269\u5b66\u6570\u636e"},"content":{"rendered":"

R\u8bed\u8a00\u5305generics\u5728\u751f\u7269\u5b66\u9886\u57df\u4e2d\u53d1\u6325\u7740\u91cd\u8981\u7684\u4f5c\u7528\uff0c\u63d0\u4f9b\u4e86\u4e00\u79cd\u901a\u7528\u7684\u65b9\u6cd5\u6765\u5b9a\u4e49\u51fd\u6570\uff0c\u4f7f\u5f97\u7528\u6237\u53ef\u4ee5\u5728\u4e0d\u540c\u7c7b\u578b\u7684\u6570\u636e\u4e0a\u4f7f\u7528\u76f8\u540c\u7684\u51fd\u6570\u540d\u79f0\uff0c\u4ece\u800c\u7b80\u5316\u4e86\u4ee3\u7801\u7684\u7f16\u5199\u548c\u7406\u89e3\u3002\u5728\u751f\u7269\u5b66\u9886\u57df\uff0c\u7814\u7a76\u4eba\u5458\u901a\u5e38\u9700\u8981\u5904\u7406\u5404\u79cd\u5404\u6837\u7684\u6570\u636e\u7c7b\u578b\uff0c\u6bd4\u5982\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u3001\u86cb\u767d\u8d28\u7ed3\u6784\u6570\u636e\u3001\u751f\u7269\u56fe\u50cf\u6570\u636e\u7b49\u3002\u6bcf\u79cd\u7c7b\u578b\u7684\u6570\u636e\u90fd\u53ef\u80fd\u9700\u8981\u7279\u5b9a\u7684\u5904\u7406\u65b9\u6cd5\u548c\u5206\u6790\u5de5\u5177\u3002<\/p>\n

generics\u5305\u5141\u8bb8\u7528\u6237\u4e3a\u4e0d\u540c\u7c7b\u578b\u7684\u6570\u636e\u5b9a\u4e49\u901a\u7528\u51fd\u6570\u3002\u901a\u8fc7\u7b80\u5355\u660e\u4e86\u7684\u65b9\u6cd5\uff0c\u7528\u6237\u53ef\u4ee5\u4e3a\u6bcf\u79cd\u6570\u636e\u7c7b\u578b\u7f16\u5199\u7279\u5b9a\u7684\u5b9e\u73b0\u4ee3\u7801\u3002\u8fd9\u4e9b\u5b9e\u73b0\u4ee3\u7801\u53ef\u4ee5\u88ab\u7edf\u4e00\u7684\u51fd\u6570\u8c03\u7528\u6240\u590d\u7528\uff0c\u65e0\u9700\u591a\u6b21\u5b9a\u4e49\u76f8\u540c\u7684\u529f\u80fd\u3002\u8fd9\u79cd\u505a\u6cd5\u4e0d\u4ec5\u5927\u5927\u51cf\u5c11\u4e86\u4ee3\u7801\u91cf\uff0c\u8fd8\u63d0\u9ad8\u4e86\u4ee3\u7801\u7684\u53ef\u8bfb\u6027\u548c\u53ef\u7ef4\u62a4\u6027\u3002<\/p>\n

\u8981\u4f7f\u7528generics\u5305\uff0c\u53ef\u4ee5\u5728R\u4e2d\u4f7f\u7528\u4ee5\u4e0b\u547d\u4ee4\u8fdb\u884c\u5b89\u88c5\u548c\u52a0\u8f7d\uff1a<\/p>\n

> install.packages(“generics”) #\u5b89\u88c5generics\u8bed\u8a00\u5305<\/p>\n

> library(generics) #\u52a0\u8f7d\u8bed\u8a00\u5305<\/p>\n

\u5728\u751f\u7269\u5b66\u4e2d\uff0c\u4e00\u4e2a\u5e38\u89c1\u7684\u4f8b\u5b50\u662f\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u7684\u5904\u7406\u548c\u5206\u6790\u3002\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u901a\u5e38\u4ee5\u77e9\u9635\u7684\u5f62\u5f0f\u8868\u793a\uff0c\u884c\u8868\u793a\u57fa\u56e0\uff0c\u5217\u8868\u793a\u6837\u672c\uff0c\u6bcf\u4e2a\u5143\u7d20\u8868\u793a\u57fa\u56e0\u5728\u7279\u5b9a\u6837\u672c\u4e2d\u7684\u8868\u8fbe\u6c34\u5e73\u3002\u4f7f\u7528generics\u5305\uff0c\u53ef\u4ee5\u5b9a\u4e49\u4e00\u4e2a\u901a\u7528\u7684\u51fd\u6570\u6765\u8ba1\u7b97\u57fa\u56e0\u8868\u8fbe\u77e9\u9635\u7684\u5e73\u5747\u8868\u8fbe\u6c34\u5e73\u3002\u7136\u540e\uff0c\u6839\u636e\u5177\u4f53\u9700\u8981\uff0c\u7528\u6237\u53ef\u4ee5\u4e3a\u4e0d\u540c\u7c7b\u578b\u7684\u57fa\u56e0\u8868\u8fbe\u6570\u636e\uff08\u4f8b\u5982RNA-seq\u6570\u636e\u548cmicroarray\u6570\u636e\uff09\u7f16\u5199\u7279\u5b9a\u7684\u5b9e\u73b0\u4ee3\u7801\uff0c\u4ee5\u9002\u5e94\u4e0d\u540c\u7684\u6570\u636e\u7ed3\u6784\u548c\u683c\u5f0f\u3002<\/p>\n

\u793a\u4f8b\uff1a<\/p>\n

# \u5b89\u88c5\u5e76\u52a0\u8f7dgenerics\u5305<\/p>\n

> install.packages(“generics”)<\/p>\n

> library(generics)<\/p>\n

# \u5b9a\u4e49\u4e00\u4e2a\u901a\u7528\u51fd\u6570\uff0c\u4f7f\u7528generics\u5305\u63d0\u4f9b\u7684generics::defmethod\u6765\u5b9a\u4e49\u4e0d\u540c\u6570\u636e\u7c7b\u578b\u7684\u5b9e\u73b0\u65b9\u6cd5<\/p>\n

> calculate_mean_expression <- generics::defmethod(function(expression_matrix) {<\/p>\n

# \u5728\u8fd9\u91cc\u5b9e\u73b0\u8ba1\u7b97\u5e73\u5747\u8868\u8fbe\u6c34\u5e73\u7684\u4ee3\u7801<\/p>\n

# \u5047\u8bbeexpression_matrix\u662f\u4e00\u4e2a\u57fa\u56e0\u8868\u8fbe\u77e9\u9635\uff0c\u5176\u4e2d\u884c\u8868\u793a\u57fa\u56e0\uff0c\u5217\u8868\u793a\u6837\u672c<\/p>\n

# …<\/p>\n

# \u8fd4\u56de\u6bcf\u4e2a\u57fa\u56e0\u7684\u5e73\u5747\u8868\u8fbe\u6c34\u5e73<\/p>\n

# …<\/p>\n

})<\/p>\n

# \u4f7f\u7528S3\u5bf9\u8c61\u7cfb\u7edf\u4e3a\u4e0d\u540c\u6570\u636e\u7c7b\u578b\u5b9a\u4e49\u5b9e\u73b0\u65b9\u6cd5<\/p>\n

> calculate_mean_expression.default <- function(expression_matrix) {<\/p>\n

# \u9ed8\u8ba4\u5b9e\u73b0\u9002\u7528\u4e8e\u4e00\u822c\u7684\u57fa\u56e0\u8868\u8fbe\u77e9\u9635<\/p>\n

# \u5728\u8fd9\u91cc\u5b9e\u73b0\u8ba1\u7b97\u5e73\u5747\u8868\u8fbe\u6c34\u5e73\u7684\u4ee3\u7801<\/p>\n

# …<\/p>\n

# \u8fd4\u56de\u6bcf\u4e2a\u57fa\u56e0\u7684\u5e73\u5747\u8868\u8fbe\u6c34\u5e73<\/p>\n

# …<\/p>\n

}<\/p>\n

> calculate_mean_expression.RNAseq <- function(expression_matrix) {<\/p>\n

# RNA-seq\u6570\u636e\u7684\u5904\u7406\u4ee3\u7801<\/p>\n

# \u5728\u8fd9\u91cc\u5b9e\u73b0\u8ba1\u7b97\u5e73\u5747\u8868\u8fbe\u6c34\u5e73\u7684\u4ee3\u7801<\/p>\n

# …<\/p>\n

# \u8fd4\u56de\u6bcf\u4e2a\u57fa\u56e0\u7684\u5e73\u5747\u8868\u8fbe\u6c34\u5e73<\/p>\n

# …<\/p>\n

}<\/p>\n

> calculate_mean_expression.microarray <- function(expression_matrix) {<\/p>\n

# microarray\u6570\u636e\u7684\u5904\u7406\u4ee3\u7801<\/p>\n

# \u5728\u8fd9\u91cc\u5b9e\u73b0\u8ba1\u7b97\u5e73\u5747\u8868\u8fbe\u6c34\u5e73\u7684\u4ee3\u7801<\/p>\n

# …<\/p>\n

# \u8fd4\u56de\u6bcf\u4e2a\u57fa\u56e0\u7684\u5e73\u5747\u8868\u8fbe\u6c34\u5e73<\/p>\n

# …<\/p>\n

}<\/p>\n

\"1_X_cedUDJvbmcIa685jzkNA\"<\/p>\n

\"1_XzKjtc0R8SHCGRBIQrltHw\"<\/p>\n

\u9664\u4e86\u57fa\u56e0\u8868\u8fbe\u6570\u636e\uff0cgenerics\u5305\u5728\u751f\u7269\u5b66\u4e2d\u8fd8\u53ef\u4ee5\u5e94\u7528\u4e8e\u8bb8\u591a\u5176\u4ed6\u9886\u57df\u3002\u4f8b\u5982\uff0c\u5728\u86cb\u767d\u8d28\u7ed3\u6784\u6570\u636e\u7684\u5206\u6790\u4e2d\uff0c\u53ef\u4ee5\u4f7f\u7528generics\u5305\u6765\u5b9a\u4e49\u4e00\u4e2a\u901a\u7528\u7684\u51fd\u6570\u6765\u8ba1\u7b97\u86cb\u767d\u8d28\u7684\u4e8c\u7ea7\u7ed3\u6784\u542b\u91cf\u3002\u7136\u540e\uff0c\u9488\u5bf9\u4e0d\u540c\u7c7b\u578b\u7684\u86cb\u767d\u8d28\u7ed3\u6784\u6570\u636e\uff08\u4f8b\u5982X\u5c04\u7ebf\u6676\u4f53\u5b66\u548c\u6838\u78c1\u5171\u632f\u6570\u636e\uff09\uff0c\u53ef\u4ee5\u7f16\u5199\u5177\u4f53\u7684\u5b9e\u73b0\u4ee3\u7801\uff0c\u4ee5\u6ee1\u8db3\u4e0d\u540c\u6570\u636e\u7c7b\u578b\u7684\u5904\u7406\u8981\u6c42\u3002<\/p>\n

\u793a\u4f8b\uff1a<\/p>\n

> install.packages(\u201cgenerics\u201d)<\/p>\n

> library(generics)<\/p>\n

> fred.default <- function(x) {<\/p>\n

+ cat(“in fred.default\\n”)<\/p>\n

+ invisible(NULL)<\/p>\n

+ }<\/p>\n

> fred(1:4)<\/p>\n

> fred.foo <- function(x) {<\/p>\n

+ cat(“in fred.foo\\n”)<\/p>\n

+ invisible(NULL)<\/p>\n

+ }<\/p>\n

> o <- 1:4<\/p>\n

> class(o) <- “foo”<\/p>\n

> fred(o)<\/p>\n

> fred.bar <- function(x) {<\/p>\n

+ cat(“in fred.bar\\n”)<\/p>\n

+ invisible(NULL)<\/p>\n

+ }<\/p>\n

> class(o) <- c(“foo”, “bar”)<\/p>\n

> fred(o)<\/p>\n

> fred(structure(1:4, class = “bar”))<\/p>\n

> myclass <- “lm”<\/p>\n

> myregex <- paste(“\\\\.”, myclass, “$”, sep = “”)<\/p>\n

> noo <- ls(envir = as.environment(“package:stats”))<\/p>\n

> loo <- grep(myregex, noo, value = TRUE)<\/p>\n

> goo <- sub(myregex, “”, loo)<\/p>\n

> sapply(goo, function(x) !is.null(getS3method(x, myclass, optional = TRUE)))<\/p>\n

confint dummy.coef model.matrix predict residuals summary<\/p>\n

TRUE TRUE TRUE TRUE TRUE TRUE<\/p>\n

> library(gmp)<\/p>\n

> foo <- as.bigq(1:10, 11:20)<\/p>\n

> foo<\/p>\n

Big Rational (‘bigq’) object of length 10:<\/p>\n

[1] 1\/11 1\/6 3\/13 2\/7 1\/3 3\/8 7\/17 4\/9 9\/19 1\/2<\/p>\n

> bar <- as.bigq(6:15, 16:25)<\/p>\n

> bar<\/p>\n

Big Rational (‘bigq’) object of length 10:<\/p>\n

[1] 3\/8 7\/17 4\/9 9\/19 1\/2 11\/21 6\/11 13\/23 7\/12 3\/5<\/p>\n

> foo + bar<\/p>\n

Big Rational (‘bigq’) object of length 10:<\/p>\n

[1] 41\/88 59\/102 79\/117 101\/133 5\/6 151\/168 179\/187 209\/207 241\/228 11\/10<\/p>\n

> foo * bar<\/p>\n

Big Rational (‘bigq’) object of length 10:<\/p>\n

[1] 3\/88 7\/102 4\/39 18\/133 1\/6 11\/56 42\/187 52\/207 21\/76 3\/10<\/p>\n

> foo \/ bar<\/p>\n

Big Rational (‘bigq’) object of length 10:<\/p>\n

[1] 8\/33 17\/42 27\/52 38\/63 2\/3 63\/88 77\/102 92\/117 108\/133 5\/6<\/p>\n

> set.seed(42)<\/p>\n

> as.bigq(rnorm(5))<\/p>\n

Big Rational (‘bigq’) object of length 5:<\/p>\n

[1] 3087123975855085\/2251799813685248 -5086348948552451\/9007199254740992 1635384977986481\/4503599627370496<\/p>\n

[4] 2850159791879263\/4503599627370496 3641325338910997\/9007199254740992<\/p>\n

> foo + 1<\/p>\n

Big Rational (‘bigq’) object of length 10:<\/p>\n

[1] 12\/11 7\/6 16\/13 9\/7 4\/3 11\/8 24\/17 13\/9 28\/19 3\/2<\/p>\n

> foo ^ 2<\/p>\n

Big Rational (‘bigq’) object of length 10:<\/p>\n

[1] 1\/121 1\/36 9\/169 4\/49 1\/9 9\/64 49\/289 16\/81 81\/361 1\/4<\/p>\n

\"Generic-L-curve-analysis-log-log-plot-of-the-cost-function-J-with-respect-to-a\"<\/p>\n

\u4ee5\u4e0a\u5c31\u662f\u5bf9R\u8bed\u8a00\u5305generics\u7684\u7b80\u5355\u4ecb\u7ecd\u5566\uff0cR\u8bed\u8a00\u5305generics\u901a\u8fc7\u63d0\u4f9b\u901a\u7528\u51fd\u6570\u7684\u5b9a\u4e49\u548c\u4f7f\u7528\uff0c\u5b83\u7b80\u5316\u4e86\u751f\u7269\u5b66\u6570\u636e\u5904\u7406\u548c\u5206\u6790\u7684\u7f16\u5199\u8fc7\u7a0b\uff0c\u51cf\u5c11\u4e86\u4ee3\u7801\u5197\u4f59\uff0c\u63d0\u9ad8\u4e86\u4ee3\u7801\u7684\u53ef\u8bfb\u6027\u548c\u53ef\u7ef4\u62a4\u6027\u3002\u751f\u7269\u5b66\u7814\u7a76\u4eba\u5458\u53ef\u4ee5\u5229\u7528\u8fd9\u4e00\u5de5\u5177\u5305\uff0c\u66f4\u52a0\u4e13\u6ce8\u4e8e\u6570\u636e\u5206\u6790\u548c\u79d1\u5b66\u53d1\u73b0\uff0c\u4e3a\u751f\u7269\u5b66\u7814\u7a76\u7684\u8fdb\u5c55\u8d21\u732e\u81ea\u5df1\u7684\u529b\u91cf\u3002<\/p>\n

\u5c0f\u4f19\u4f34\u4eec\uff0c\u4eca\u5929\u6709\u6ca1\u6709\u5b66\u5230\u65b0\u77e5\u8bc6\u5462\uff0c\u60f3\u8981\u7ee7\u7eed\u4e86\u89e3R\u8bed\u8a00\u5185\u5bb9\u53ef\u4ee5\u6301\u7eed\u5173\u6ce8\u5c0f\u679c\u54e6\uff5e\uff5e\u6216\u8005\u4e5f\u53ef\u4ee5\u5173\u6ce8\u6211\u4eec\u7684\u5b98\u7f51\u4e5f\u4f1a\u6301\u7eed\u66f4\u65b0\u7684\u54e6\uff5e http:\/\/www.biocloudservice.com\/home.html<\/a><\/p>\n

References:<\/p>\n

    \n
  1. https:\/\/www.stat.umn.edu\/geyer\/3701\/notes\/generic.html<\/a><\/li>\n
  2. https:\/\/www.google.com\/url?sa=i&url=https%3A%2F%2Fmedium.com%2F%40gauravgada%2Fim-going-to-stop-using-generic-x-y-plotting-in-r-85f017b49409&psig=AOvVaw39GTCAH8-yF7F0UkyMvU_0&ust=1690278705856000&source=images&cd=vfe&opi=89978449&ved=0CBAQjRxqFwoTCLDJlYGJp4ADFQAAAAAdAAAAABAE<\/a><\/li>\n
  3. https:\/\/www.google.com\/url?sa=i&url=https%3A%2F%2Fwww.researchgate.net%2Ffigure%2FGeneric-L-curve-analysis-log-log-plot-of-the-cost-function-J-with-respect-to-a_fig4_281567420&psig=AOvVaw39GTCAH8-yF7F0UkyMvU_0&ust=1690278705856000&source=images&cd=vfe&opi=89978449&ved=0CBAQjRxqFwoTCLDJlYGJp4ADFQAAAAAdAAAAABAh<\/a><\/li>\n
  4. https:\/\/www.google.com\/url?sa=i&url=https%3A%2F%2Fmedium.com%2F%40gauravgada%2Fim-going-to-stop-using-generic-x-y-plotting-in-r-85f017b49409&psig=AOvVaw39GTCAH8-yF7F0UkyMvU_0&ust=1690278705856000&source=images&cd=vfe&opi=89978449&ved=0CBAQjRxqFwoTCLDJlYGJp4ADFQAAAAAdAAAAABAp<\/a><\/li>\n<\/ol>\n","protected":false},"excerpt":{"rendered":"

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