updated

BronchiCellPred.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: ASCII
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source

DESCRIPTION

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+Package: BronchiCellPred
+Type: Package
+Title: BronchiCellPred
+Version: 0.1.0
+Author: Cancan Qi
+Maintainer: Cancan Qi <tracyqican@gmail.com>
+Description: 
+    BronchiCellPred is used to predict cell proportion of bronchial biopies using bulk gene expression data.
+License: GPL-3
+Encoding: UTF-8
+LazyData: true
+Imports: Seurat, tidyverse, reshape2, xbioc, MuSiC, bseqsc, ggplot2
+RoxygenNote: 7.1.1

NAMESPACE

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+exportPattern("^[[:alpha:]]+")

R/analysis.R

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+
+#' main function of this package, to calculate cell proportion
+#'
+#' @param bulk.eset ExpressionSet for bulk data, raw counts as the input
+#' @param method Three deconvolution methods are provided: MuSiC, NNLS and bseqsc (based on CIBERSORT), MuSiC is the defual method
+#' @return est.prop, A cell proportion matrix, each row represent a sample, each col is a cell type
+#' @import tidyverse, reshape2, xbioc, MuSiC,bseqsc
+#' @export
+#'
+BronCell.prop<-function(bulk.eset,method="MuSiC"){
+
+  if(!exists("sc.basis")){
+    data(sc.basis)
+  }
+
+  if(method=="MuSiC"){
+    Est.prop<-music_prop_bron(bulk.eset = bulk.eset, sc.basis = sc.basis, clusters = 'cellType',
+                                samples = 'sampleID', verbose = F)
+
+    est_prop<-as.data.frame(Est.prop$Est.prop.weighted)
+
+  } else if (method=="nnls"){
+    Est.prop<-music_prop_bron(bulk.eset = bulk.eset, sc.basis = sc.basis, clusters = 'cellType',
+                                samples = 'sampleID', verbose = F)
+
+    est_prop<-as.data.frame(Est.prop$Est.prop.allgene)
+  } else if (method=="bseq"){
+    fit <- bseqsc_proportions(bulk.eset, sc.basis$M.theta, verbose = TRUE)
+    est_prop<-as.data.frame(t(coef(fit)))
+  }
+
+  return(est_prop)
+}
+
+
+#' plot cell proporions for each bronchial cell types
+#' @param est_prop cell proportion matrix, estimated by funtion BronCell.prop
+#' @import tidyverse, reshape2
+#' @export
+BronCell.plot<-function(est_prop){
+  est_prop$id<-rownames(est_prop)
+  df1<-melt(est_prop,id.vars = "id")
+  colnames(df1)<-c("ID","Cell_type","Estimated_proportion")
+  plot<-ggplot(df1, aes(x = Cell_type, y = Estimated_proportion,fill=Cell_type)) +
+    geom_boxplot()+geom_jitter(size=0.5)+
+    theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
+          panel.background = element_blank(), axis.line = element_line(colour = "black"),
+          axis.text.x=element_text(angle=45, hjust=1))
+
+  return(plot)
+}
+
+
+#' modified function of "music_prop" from MuSiC package using the signature matrix as the input
+#' original code is on: https://github.com/xuranw/MuSiC
+#'
+#' This function is to calculate the MuSiC deconvolution proportions
+#'
+#' @param bulk.eset ExpressionSet for bulk data
+#' @param sc.basis Gene signature matrix generated from bronchial biopsy scRNAseq data, using function music_basis from MuSiC package
+#' @param clusters character, the phenoData of single cell dataset used as clusters;
+#' @param samples character,the phenoData of single cell dataset used as samples;
+#' @param select.ct vector of cell types, default as NULL. If NULL, then use all cell types provided by single cell dataset;
+#' @param cell_size data.frame of cell sizes. 1st column contains the names of cell types, 2nd column has the cell sizes per cell type. Default as NULL. If NULL, then estimate cell size from data;
+#' @param ct.cov logical. If TRUE, use the covariance across cell types;
+#' @param verbose logical, default as TRUE.
+#' @param iter.max numeric, maximum iteration number
+#' @param nu regulation parameter, take care of weight when taking recipical
+#' @param eps Thredshold of convergence
+#' @param centered logic, substract avg of Y and D
+#' @param normalize logic, divide Y and D by their standard deviation
+#' @return a list with elements:
+#'    * Estimates of MuSiC
+#'    * Estimates of NNLS
+#'    * Weight of MuSiC
+#'    * r.squared of MuSiC
+#'    * Variance of MuSiC estimates
+#' @export
+music_prop_bron = function(bulk.eset, sc.basis, clusters, samples, select.ct = NULL, cell_size = NULL, ct.cov = FALSE, verbose = TRUE,
+                           iter.max = 1000, nu = 0.0001, eps = 0.01, centered = FALSE, normalize = FALSE, ... ){
+
+  bulk.gene = rownames(bulk.eset)[rowMeans(exprs(bulk.eset)) != 0]
+  bulk.eset = bulk.eset[bulk.gene, , drop = FALSE]
+  markers<-rownames(sc.basis$Disgn.mtx)
+  cm.gene = intersect( rownames(sc.basis$Disgn.mtx), bulk.gene )
+
+  if(length(cm.gene)< 0.2*length(markers))
+    stop("Too few common genes!")
+
+  if(verbose){message(paste('Used', length(cm.gene), 'common genes...'))}
+
+  m.sc = match(cm.gene, rownames(sc.basis$Disgn.mtx)); m.bulk = match(cm.gene, bulk.gene)
+  D1 = sc.basis$Disgn.mtx[m.sc, ];
+  M.S = colMeans(sc.basis$S, na.rm = T);
+
+  if(!is.null(cell_size)){
+    if(!is.data.frame(cell_size)){
+      stop("cell_size paramter should be a data.frame with 1st column for cell type names and 2nd column for cell sizes")
+    }else if(sum(names(M.S) %in% cell_size[, 1]) != length(names(M.S))){
+      stop("Cell type names in cell_size must match clusters")
+    }else if (any(is.na(as.numeric(cell_size[, 2])))){
+      stop("Cell sizes should all be numeric")
+    }
+    my_ms_names <- names(M.S)
+    cell_size <- cell_size[my_ms_names %in% cell_size[, 1], ]
+    M.S <- cell_size[match(my_ms_names, cell_size[, 1]),]
+    M.S <- M.S[, 2]
+    names(M.S) <- my_ms_names
+  }
+
+  Yjg = relative.ab(exprs(bulk.eset)[m.bulk, ]); N.bulk = ncol(bulk.eset);
+  if(ct.cov){
+    Sigma.ct = sc.basis$Sigma.ct[, m.sc];
+
+    Est.prop.allgene = NULL
+    Est.prop.weighted = NULL
+    Weight.gene = NULL
+    r.squared.full = NULL
+    Var.prop = NULL
+
+    for(i in 1:N.bulk){
+      if(sum(Yjg[, i] == 0) > 0){
+        D1.temp = D1[Yjg[, i]!=0, ];
+        Yjg.temp = Yjg[Yjg[, i]!=0, i];
+        Sigma.ct.temp = Sigma.ct[, Yjg[,i]!=0];
+        if(verbose) message(paste(colnames(Yjg)[i], 'has common genes', sum(Yjg[, i] != 0), '...') )
+      }else{
+        D1.temp = D1;
+        Yjg.temp = Yjg[, i];
+        Sigma.ct.temp = Sigma.ct;
+        if(verbose) message(paste(colnames(Yjg)[i], 'has common genes', sum(Yjg[, i] != 0), '...'))
+      }
+
+      lm.D1.weighted = music.iter.ct(Yjg.temp, D1.temp, M.S, Sigma.ct.temp, iter.max = iter.max,
+                                     nu = nu, eps = eps, centered = centered, normalize = normalize)
+      Est.prop.allgene = rbind(Est.prop.allgene, lm.D1.weighted$p.nnls)
+      Est.prop.weighted = rbind(Est.prop.weighted, lm.D1.weighted$p.weight)
+      weight.gene.temp = rep(NA, nrow(Yjg)); weight.gene.temp[Yjg[,i]!=0] = lm.D1.weighted$weight.gene;
+      Weight.gene = cbind(Weight.gene, weight.gene.temp)
+      r.squared.full = c(r.squared.full, lm.D1.weighted$R.squared)
+      Var.prop = rbind(Var.prop, lm.D1.weighted$var.p)
+    }
+  }else{
+    Sigma = sc.basis$Sigma[m.sc, ];
+
+    valid.ct = (colSums(is.na(Sigma)) == 0)&(colSums(is.na(D1)) == 0)&(!is.na(M.S))
+
+    if(sum(valid.ct)<=1){
+      stop("Not enough valid cell type!")
+    }
+
+    if(verbose){message(paste('Used', sum(valid.ct), 'cell types in deconvolution...' ))}
+
+    D1 = D1[, valid.ct]; M.S = M.S[valid.ct]; Sigma = Sigma[, valid.ct];
+
+    Est.prop.allgene = NULL
+    Est.prop.weighted = NULL
+    Weight.gene = NULL
+    r.squared.full = NULL
+    Var.prop = NULL
+    for(i in 1:N.bulk){
+      if(sum(Yjg[, i] == 0) > 0){
+        D1.temp = D1[Yjg[, i]!=0, ];
+        Yjg.temp = Yjg[Yjg[, i]!=0, i];
+        Sigma.temp = Sigma[Yjg[,i]!=0, ];
+        if(verbose) message(paste(colnames(Yjg)[i], 'has common genes', sum(Yjg[, i] != 0), '...') )
+      }else{
+        D1.temp = D1;
+        Yjg.temp = Yjg[, i];
+        Sigma.temp = Sigma;
+        if(verbose) message(paste(colnames(Yjg)[i], 'has common genes', sum(Yjg[, i] != 0), '...'))
+      }
+
+      lm.D1.weighted = music.iter(Yjg.temp, D1.temp, M.S, Sigma.temp, iter.max = iter.max,
+                                  nu = nu, eps = eps, centered = centered, normalize = normalize)
+      Est.prop.allgene = rbind(Est.prop.allgene, lm.D1.weighted$p.nnls)
+      Est.prop.weighted = rbind(Est.prop.weighted, lm.D1.weighted$p.weight)
+      weight.gene.temp = rep(NA, nrow(Yjg)); weight.gene.temp[Yjg[,i]!=0] = lm.D1.weighted$weight.gene;
+      Weight.gene = cbind(Weight.gene, weight.gene.temp)
+      r.squared.full = c(r.squared.full, lm.D1.weighted$R.squared)
+      Var.prop = rbind(Var.prop, lm.D1.weighted$var.p)
+    }
+  }
+  colnames(Est.prop.weighted) = colnames(D1)
+  rownames(Est.prop.weighted) = colnames(Yjg)
+  colnames(Est.prop.allgene) = colnames(D1)
+  rownames(Est.prop.allgene) = colnames(Yjg)
+  names(r.squared.full) = colnames(Yjg)
+  colnames(Weight.gene) = colnames(Yjg)
+  rownames(Weight.gene) = cm.gene
+  colnames(Var.prop) = colnames(D1)
+  rownames(Var.prop) = colnames(Yjg)
+
+  return(list(Est.prop.weighted = Est.prop.weighted, Est.prop.allgene = Est.prop.allgene,
+              Weight.gene = Weight.gene, r.squared.full = r.squared.full, Var.prop = Var.prop))
+}
+
+

R/data.R

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+########
+#### Documentation of data in the deconCell package
+########
+
+
+#' gene signature matrix used for predicting cell proportion from bulk RNAseq data
+#' generated from MuSiC fuction 'musci_basis'
+#' @format a music basis object with signature matrix before and after scaling, names are coded in gene symbol
+"sc.basis"

R/hello.R

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+# Hello, world!
+#
+# This is an example function named 'hello' 
+# which prints 'Hello, world!'.
+#
+# You can learn more about package authoring with RStudio at:
+#
+#   http://r-pkgs.had.co.nz/
+#
+# Some useful keyboard shortcuts for package authoring:
+#
+#   Build and Reload Package:  'Cmd + Shift + B'
+#   Check Package:             'Cmd + Shift + E'
+#   Test Package:              'Cmd + Shift + T'
+
+hello <- function() {
+  print("Hello, world!")
+}

man/BronCell.plot.Rd

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/analysis.R
+\name{BronCell.plot}
+\alias{BronCell.plot}
+\title{plot cell proporions for each bronchial cell types}
+\usage{
+BronCell.plot(est_prop)
+}
+\arguments{
+\item{est_prop}{cell proportion matrix, estimated by funtion BronCell.prop}
+}
+\description{
+plot cell proporions for each bronchial cell types
+}

man/BronCell.prop.Rd

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/analysis.R
+\name{BronCell.prop}
+\alias{BronCell.prop}
+\title{main function of this package, to calculate cell proportion}
+\usage{
+BronCell.prop(bulk.eset, method = "MuSiC")
+}
+\arguments{
+\item{bulk.eset}{ExpressionSet for bulk data, raw counts as the input}
+
+\item{method}{Three deconvolution methods are provided: MuSiC, NNLS and bseqsc (based on CIBERSORT), MuSiC is the defual method}
+}
+\value{
+est.prop, A cell proportion matrix, each row represent a sample, each col is a cell type
+}
+\description{
+main function of this package, to calculate cell proportion
+}

man/hello.Rd

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+\name{hello}
+\alias{hello}
+\title{Hello, World!}
+\usage{
+hello()
+}
+\description{
+Prints 'Hello, world!'.
+}
+\examples{
+hello()
+}

man/music_prop_bron.Rd

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/analysis.R
+\name{music_prop_bron}
+\alias{music_prop_bron}
+\title{modified function of "music_prop" from MuSiC package using the signature matrix as the input
+original code is on: https://github.com/xuranw/MuSiC}
+\usage{
+music_prop_bron(
+  bulk.eset,
+  sc.basis,
+  clusters,
+  samples,
+  select.ct = NULL,
+  cell_size = NULL,
+  ct.cov = FALSE,
+  verbose = TRUE,
+  iter.max = 1000,
+  nu = 1e-04,
+  eps = 0.01,
+  centered = FALSE,
+  normalize = FALSE,
+  ...
+)
+}
+\arguments{
+\item{bulk.eset}{ExpressionSet for bulk data}
+
+\item{sc.basis}{Gene signature matrix generated from bronchial biopsy scRNAseq data, using function music_basis from MuSiC package}
+
+\item{clusters}{character, the phenoData of single cell dataset used as clusters;}
+
+\item{samples}{character,the phenoData of single cell dataset used as samples;}
+
+\item{select.ct}{vector of cell types, default as NULL. If NULL, then use all cell types provided by single cell dataset;}
+
+\item{cell_size}{data.frame of cell sizes. 1st column contains the names of cell types, 2nd column has the cell sizes per cell type. Default as NULL. If NULL, then estimate cell size from data;}
+
+\item{ct.cov}{logical. If TRUE, use the covariance across cell types;}
+
+\item{verbose}{logical, default as TRUE.}
+
+\item{iter.max}{numeric, maximum iteration number}
+
+\item{nu}{regulation parameter, take care of weight when taking recipical}
+
+\item{eps}{Thredshold of convergence}
+
+\item{centered}{logic, substract avg of Y and D}
+
+\item{normalize}{logic, divide Y and D by their standard deviation}
+}
+\value{
+a list with elements:
+   * Estimates of MuSiC
+   * Estimates of NNLS
+   * Weight of MuSiC
+   * r.squared of MuSiC
+   * Variance of MuSiC estimates
+}
+\description{
+This function is to calculate the MuSiC deconvolution proportions
+}

man/sc.basis.Rd

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data.R
+\docType{data}
+\name{sc.basis}
+\alias{sc.basis}
+\title{gene signature matrix used for predicting cell proportion from bulk RNAseq data
+generated from MuSiC fuction 'musci_basis'}
+\format{
+a music basis object with signature matrix before and after scaling, names are coded in gene symbol
+}
+\usage{
+sc.basis
+}
+\description{
+gene signature matrix used for predicting cell proportion from bulk RNAseq data
+generated from MuSiC fuction 'musci_basis'
+}
+\keyword{datasets}