Merge pull request #1 from ysora90/0

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DESCRIPTION

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+Package: bimir
+Type: Package
+Title: Condition-Specific microRNA Target Prediction by Biclustering of Large Transcriptome Data 
+Version: 1.0
+Author: Sora Yoon
+Maintainer: Sora Yoon <[email protected]>
+Description: Generates biclusters provided in BIMIR website <http://btools.org/bimir_dir>, which is a bicluster database that provides the condition-specific microRNA target predictions. Because miRNAs repress the gene expression post-transcriptionally, mRNA-miRNA paired profilings have been commonly used to predict the condition-specific miRNA targets. However, it is costly, and hence, there are not many publicly available mRNA-miRNA paired profilings for various cell conditions. In this study, we solved these problems by utilizing a large collection of public mRNA microarray data. Using the data, we created a matrix of fold change (FC) values for 20,639 human genes in 5,158 cell conditions (test vs. control group). By biclustering this matrix, we derived 29,815 biclusters for 451 microRNAs. To create these biclusters, first we extracted the initial seed biclusters full of signals (e.g., FC>1.3), and progressively extended them using PBE algorithm including a small number of noises. This process resulted in large and quite dense biclusters compared to those generated by other existing methods. 
+License: GPL-2
+Encoding: UTF-8
+LazyData: true
+RoxygenNote: 6.0.1
+Depends: biclust

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(PBE)
+export(PBE_MERGE)
+export(bicluster_extension_process)
+export(bicluster_trimming_process)
+export(getGenelist)
+export(getMIRprofile)
+export(get_miR_target)
+export(get_zero_rate)
+export(getmiRNAlist)
+export(load_FCtable)
+export(make_biclust)
+export(merge_bicluster)
+import(biclust)
+import(stats)
+import(utils)

R/MIRprofile_from_FCtable.R

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+#'@title load_FCtable
+#'
+#'@description Loading a large table of fold change values for 20,639 human genes in 5,158 cell conditions.
+#'@return A fold change matrix of 5,158 rows and 20,639 columns.
+#'@export
+load_FCtable = function()
+{
+  cat('FC matrix is now loading ...\n')
+  f = system.file('extdata', 'FC1.rds', package = 'bimir')
+  fc = readRDS(f)
+  cat("1/10\n")
+  for(i in 2:10)
+  {
+  	f = system.file('extdata', paste('FC',i,'.rds',sep=""), package = 'bimir')
+  	fc_temp = readRDS(f)
+  	fc = cbind(fc,fc_temp)
+ 	cat(i,"/10\n",sep="")
+  }
+  cat('Loaded!\n')
+  return(fc)
+}
+
+#'@title Load human gene list
+#'@description 20,639 human genes
+#'@return A vector of 20,639 human genes
+#'@export
+#'@import utils
+getGenelist = function()
+{
+  f = system.file('extdata','genelist.rds', package='bimir')
+  genelist = readRDS(f)
+  genelist = gsub('-','.',genelist,fixed = T)
+  return(genelist)
+}
+
+#'@title Load human miRNA list
+#'@description human mature miRNA list
+#'@return A vector of 2,632 human mature miRNAs
+#'@export
+#'@import utils
+getmiRNAlist = function()
+{
+  f = system.file('extdata', 'miRNAlist.rds', package='bimir')
+  miRNAlist = readRDS(f)
+  return(miRNAlist)
+}
+
+#'@title Load human miRNA target index
+#'@description human miRNA target index
+#'@return A vector of human miRNA target index
+#'@import utils
+getAllmiRNATargetIndex = function()
+{
+  f = system.file('extdata', 'miRNATargets.rds', package='bimir')
+  index = readRDS(f)
+  return(index)
+}
+
+#'Get sequence-based miRNA targets
+#'
+#'@description Returns miRNA targets predicted from three or more algorithms.
+#'
+#'@param miRNA miRNA name. One of miRNAs listed in "miRNAlist" data.
+#'@return A vector of sequence-based miRNA targets
+#'@examples get_miR_target('hsa-miR-1-3p')
+#'@export
+get_miR_target = function(miRNA)
+{
+  genelist = getGenelist()
+  miRNAlist = getmiRNAlist()
+  miRNATargets = getAllmiRNATargetIndex()
+  mir_index = which(miRNAlist%in%miRNA)
+  if(length(mir_index)==0){stop(paste(miRNA,'is not in the miRNAlist. Type getmiRNAlist() to refer to the available miRNAs'))}
+  index_target = miRNATargets[mir_index]
+  index_target = unlist(strsplit(index_target,split="\t"))
+  index_target = as.numeric(index_target)
+  index_target = unique(index_target)
+  targets = genelist[index_target]
+  return(targets)
+}
+
+#'Get MIRprofile
+#'
+#'@description Returns MIR profile for input miRNA.
+#'
+#'@param miRNA miRNA name. One of miRNAs listed in "miRNAlist" data.
+#'@param FCtable FC matrix of 20,639 genes for 5,158 conditions. If NULL, it will be loaded from the local.
+#'@param FCcutoff Fold change cutoff in log2 scale. Default = log2(1.3). To extract MIR profile for target down-regulation in test condition, take negative value.
+#'@return A matrix of fold change value of sequence-based miRNA targets under selected cell conditions.
+#'@examples fc=load_FCtable(); MIRprofile = getMIRprofile('hsa-miR-1-3p',fc,log2(1.3))
+#'@import stats utils
+#'@export
+getMIRprofile = function(miRNA, FCtable=NULL, FCcutoff=log2(1.3))
+{
+  if(is.null(miRNA)){stop('human miRNA name must be given. Refer to the list of miRNAs from "miRNAlist" data in the package.')}
+  if(is.null(FCtable)){ FCtable = load_FCtable() }
+  if(FCcutoff==0){stop('FCcutoff must be larger or lesser than 0.')}
+  miRNAlist = getmiRNAlist()
+  genelist = getGenelist()
+  mir_index = which(miRNAlist%in%miRNA)
+  if(length(mir_index)==0){stop('There is no such microRNA in the DB. Refer to the list of miRNAs by typing getmiRNAlist().')}
+  ConditionOverlapP = function(X, seqTar, FCcut)
+  {
+    seqTar = intersect(genelist, seqTar)
+    geneidx = if(FCcutoff>0){which(X>FCcut)}else{which(X<FCcut)}
+    genes = genelist[geneidx]
+    L1 = length(intersect(genes, seqTar)) - 1
+    L2 = length(genes)
+    L3 = 20639 - L2
+    L4 = length(seqTar)
+    p = phyper(L1, L2, L3, L4, lower.tail=F)
+    p = signif(p, 4)
+    return(p)
+  }
+  MIRtargets = get_miR_target(miRNA)
+  overlapP = apply(FCtable, 1, ConditionOverlapP, seqTar = MIRtargets, FCcut = FCcutoff)
+  overlapFDR = p.adjust(overlapP, method = 'fdr')
+  signifCondition = which(overlapFDR<0.05)
+
+  result_profile = FCtable[signifCondition, MIRtargets]
+  return(result_profile)
+}
+