intial commit

.Rbuildignore

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+^.*\.Rproj$
+^\.Rproj\.user$

.gitignore

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+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata

DESCRIPTION

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+Package: imsig
+Type: Package
+Title: Immune Cell Gene Signatures for Profiling the Microenvironment of Solid Tumours
+Version: 0.1.0
+Author: Ajit Johnson Nirmal
+Maintainer: Ajit Johnson Nirmal <ajitjohnson.n@gmail.com>
+Description: Estimating relative abundance of tissue-infiltrating immune subpopulations abundances using gene expression data.
+License: MIT
+Encoding: UTF-8
+LazyData: true
+Imports:
+  HiClimR (>= 1.2.3)
+RoxygenNote: 6.0.1

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(corr_matrix)
+importFrom(HiClimR,fastCor)

R/corr_matrix.R

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+#' @title Generation of a correlation matrix
+#' @description Creates a correlation matrix using ImSig signature genes.
+#' @param exp Expression matrix with genes as rows and samples as columns [data.frame]
+#' @param r Correlation cut-off to use. Correlations below the defined cut-off will be replaced with zero before returning the final correlation matrix.
+#' @return Gene-gene correlation matrix of the ImSig genes.
+#' @importFrom HiClimR fastCor
+#' @export
+
+corr_matrix <- function(exp, r){
+  sig_su <- sig[which(as.character(sig$gene) %in% row.names(exp)), ]
+  data <- exp[as.character(sig_su$gene),]
+  cor_data <- fastCor(t(data))
+  cor_data[cor_data <= r]= 0
+  diag(cor_data) = 0
+  return(cor_data)
+}

R/sig.R

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+#' @title ImSig genes
+#' @description ImSig signature genes and the cell type they represent
+#' @name sig
+#' @docType data
+#' @usage sig
+#' @format dataframe
+#' @keywords datasets
+NULL

imsig.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageCheckArgs: --as-cran
+PackageRoxygenize: rd,collate,namespace,vignette