# #——风格,回声= FALSE,结果= '飞机 '-------------------------------------------------------- BiocStyle:减价()选项(宽度= 100,max.print = 1000) knitr:: opts_chunk设置(eval = as.logical (Sys美元。gettenv ("KNITR_EVAL"， "TRUE"))，缓存=as.logical(Sys. value)。采用“KNITR_CACHE”、“真的 "))) ## ---- 设置中,回声= FALSE,消息= FALSE,警告= FALSE -------------------------------------------- suppressPackageStartupMessages({库(ChemmineR)库(fmcsR ) }) ## ---- eval = FALSE ----------------------------------------------------------------------------------- # 如果(!requireNamespace("BiocManager"， quiet =TRUE)) # install.packages("BiocManager") # BiocManager::install("fmcsR") ## ----quicktest1, eval=TRUE, fig=TRUE,fig. package ("BiocManager")scap="样本数据的结构描述。"------------- 库(fmcsR)数据(fmcstest)情节(fmcstest[1:3],打印= FALSE) # #——quicktest2 eval = TRUE,无花果= TRUE -------------------------------------------------------------- 测试<设施管理(fmcstest [1], fmcstest[2],非盟= 2,bu = 1) plotMCS(测试,regenCoords = TRUE) # # - eval = TRUE,保持。源= TRUE ------------------------------------------------------------------ 库(fmcsR) #加载包# # - eval = FALSE,保持。源= TRUE ----------------------------------------------------------------- # 库(帮助= " fmcsR”)#列表fmcsR #库提供的函数/类(帮助=“ChemmineR”)从ChemmineR # #列表函数/类建树(fmcsR) #打开PDF手册(ChemmineR) # #一幕打开ChemmineR PDF手册# #——eval = FALSE。源= TRUE ----------------------------------------------------------------- # ? 设施管理#“MCS-class”# ?“SDFset-class”# # - eval = TRUE,保持。源= TRUE ------------------------------------------------------------------ 数据(fmcstest) sdfset < - fmcstest sdfset # #, eval = FALSE。源= TRUE ----------------------------------------------------------------- # 写。SDF(sdfset, file="sdfset. SDF ") # mysdf <- read.SDFset(file="sdfset. SDF ") ## ----eval=TRUE，保存。源= TRUE ------------------------------------------------------------------ mcsa < -设施管理(sdfset [[1]], sdfset [[2]]) mcsa mcsb < -设施管理(sdfset [[1]], sdfset [[3]]) mcsb # #, eval = TRUE。源= TRUE ------------------------------------------------------------------ sdfset设施管理(sdfset[1],[2],快= TRUE) # #, eval = TRUE。源= TRUE ------------------------------------------------------------------ slotNames (mcsa) # #, eval = TRUE。源= TRUE ------------------------------------------------------------------ 统计(mcsa) #或mcsa[["统计"]]mcsa1 < - mcs1 (mcsa) #或mcsa[[“mcs1”]]mcsa2 <——mcs2 (mcsa) #或mcsa[[“mcs2”]]mcsa1[1] #返回SDFset组件mcsa1[[2]][1:2] #返回前两个指数向量# # - eval = TRUE,无花果= TRUE。源= TRUE -------------------------------------------------------- mcstosdfset < - mcs2sdfset (mcsa、类型=“新”)情节(mcstosdfset[[1]],打印= FALSE) # #, eval = TRUE。源= TRUE ------------------------------------------------------------------ mylist < -列表(统计=统计(mcsa) mcs1 = mcs1 (mcsa) mcs2 = mcs2 (mcsa)) (MCS mylist。 ") ## ---- au0bu0 eval = TRUE,无花果= TRUE ------------------------------------------------------------------ sdfset plotMCS(设施管理(sdfset[1],[2],非盟= 0,bu = 0 )) ## ---- au1bu1 eval = TRUE,无花果= TRUE ------------------------------------------------------------------ sdfset plotMCS(设施管理(sdfset[1],[2],非盟= 1,bu = 1 )) ## ---- au2bu2 eval = TRUE,无花果= TRUE ------------------------------------------------------------------ sdfset plotMCS(设施管理(sdfset[1],[2],非盟= 2,bu = 2 )) ## ---- au0bu013 eval = TRUE,无花果= TRUE ---------------------------------------------------------------- sdfset plotMCS(设施管理(sdfset[1],[3],非盟= 0,bu = 0 )) ## ---- eval = TRUE,保持。source=TRUE------------------------------------------------------------------ data(sdfsample) # Loads larger sample data set sdf <- sdfsample fmcsBatch(sdf[1], sdf[1:30], au=0, bu=0) ## ----tree, eval=TRUE, fig=TRUE-------------------------------------------------------------------- sdf <- sdf[1:7] d <- sapply(cid(sdf), function(x) fmcsBatch(sdf[x], sdf, au=0, bu=0, matching.mode="aromatic")[,"Overlap_Coefficient"]) d hc <- hclust(as.dist(1-d), method="complete") plot(as.dendrogram(hc), edgePar=list(col=4, lwd=2), horiz=TRUE) ## ----au0bu024, eval=TRUE, fig=TRUE---------------------------------------------------------------- plotMCS(fmcs(sdf[3], sdf[7], au=0, bu=0, matching.mode="aromatic")) ## ----sessionInfo, print=TRUE--------------------------------------------------------------------- sessionInfo()