| ... | ... |
@@ -1,9 +1,9 @@ |
| 1 | 1 |
# Generated by roxygen2: do not edit by hand |
| 2 | 2 |
|
| 3 |
+export(CLR_FN) |
|
| 3 | 4 |
export(DESEQ_FN) |
| 4 | 5 |
export(FQT_FN) |
| 5 | 6 |
export(FQ_FN) |
| 6 |
-export(RLE_FN) |
|
| 7 | 7 |
export(SUM_FN) |
| 8 | 8 |
export(SconeExperiment) |
| 9 | 9 |
export(TMM_FN) |
| ... | ... |
@@ -43,7 +43,6 @@ import(methods) |
| 43 | 43 |
import(plotly) |
| 44 | 44 |
import(visNetwork) |
| 45 | 45 |
importClassesFrom(SummarizedExperiment,SummarizedExperiment) |
| 46 |
-importFrom(DESeq,estimateSizeFactorsForMatrix) |
|
| 47 | 46 |
importFrom(DT,dataTableOutput) |
| 48 | 47 |
importFrom(DT,dataTableProxy) |
| 49 | 48 |
importFrom(DT,formatSignif) |
| ... | ... |
@@ -57,6 +56,7 @@ importFrom(boot,inv.logit) |
| 57 | 56 |
importFrom(boot,logit) |
| 58 | 57 |
importFrom(class,knn) |
| 59 | 58 |
importFrom(cluster,silhouette) |
| 59 |
+importFrom(compositions,clr) |
|
| 60 | 60 |
importFrom(diptest,dip.test) |
| 61 | 61 |
importFrom(edgeR,calcNormFactors) |
| 62 | 62 |
importFrom(fpc,pamk) |
| ... | ... |
@@ -33,7 +33,7 @@ TMM_FN = function(ei) {
|
| 33 | 33 |
return(eo) |
| 34 | 34 |
} |
| 35 | 35 |
|
| 36 |
-#' Relative log-expression (RLE) scaling normalization wrapper function |
|
| 36 |
+#' Relative log-expression (RLE; DESeq) scaling normalization wrapper function |
|
| 37 | 37 |
#' @importFrom edgeR calcNormFactors |
| 38 | 38 |
#' @details SCONE scaling wrapper for \code{\link[edgeR]{calcNormFactors}}).
|
| 39 | 39 |
#' @export |
| ... | ... |
@@ -42,9 +42,9 @@ TMM_FN = function(ei) {
|
| 42 | 42 |
#' |
| 43 | 43 |
#' @examples |
| 44 | 44 |
#' ei <- matrix(0:20,nrow = 7) |
| 45 |
-#' eo <- RLE_FN(ei) |
|
| 45 |
+#' eo <- DESEQ_FN(ei) |
|
| 46 | 46 |
#' |
| 47 |
-RLE_FN = function(ei) {
|
|
| 47 |
+DESEQ_FN = function(ei) {
|
|
| 48 | 48 |
size_fac = calcNormFactors(ei, method = "RLE") |
| 49 | 49 |
scales = (colSums(ei) * size_fac) |
| 50 | 50 |
eo = t(t(ei) * mean(scales) / scales) |
| ... | ... |
@@ -100,20 +100,24 @@ FQT_FN = function(ei) {
|
| 100 | 100 |
return(eo) |
| 101 | 101 |
} |
| 102 | 102 |
|
| 103 |
-#' DESeq size factor scaling normalization wrapper function |
|
| 104 |
-#' @importFrom DESeq estimateSizeFactorsForMatrix |
|
| 103 |
+#' Centered log-ratio (CLR) normalization wrapper function |
|
| 104 |
+#' @importFrom compositions clr |
|
| 105 |
+#' @importFrom matrixStats colMedians |
|
| 105 | 106 |
#' @details SCONE scaling wrapper for |
| 106 |
-#' \code{\link[DESeq]{estimateSizeFactorsForMatrix}}).
|
|
| 107 |
+#' \code{\link[compositions]{clr}}).
|
|
| 107 | 108 |
#' @export |
| 108 | 109 |
#' @param ei Numerical matrix. (rows = genes, cols = samples). |
| 109 |
-#' @return DESeq size factor normalized matrix. |
|
| 110 |
+#' @return CLR normalized matrix. |
|
| 110 | 111 |
#' |
| 111 | 112 |
#' @examples |
| 112 | 113 |
#' ei <- matrix(0:20,nrow = 7) |
| 113 |
-#' eo <- DESEQ_FN(ei) |
|
| 114 |
+#' eo <- CLR_FN(ei) |
|
| 114 | 115 |
#' |
| 115 |
-DESEQ_FN = function(ei) {
|
|
| 116 |
- size_fac = estimateSizeFactorsForMatrix(ei) |
|
| 117 |
- eo = t(t(ei) / size_fac) |
|
| 116 |
+CLR_FN = function (ei) |
|
| 117 |
+{
|
|
| 118 |
+ scale_mat <- t(clr(t(ei))) - log(ei) |
|
| 119 |
+ scale_mat[ei == 0] = NA |
|
| 120 |
+ scales = exp(-colMedians(scale_mat, na.rm = TRUE)) |
|
| 121 |
+ eo = t(t(ei) * mean(scales) / scales) |
|
| 118 | 122 |
return(eo) |
| 119 | 123 |
} |
| 120 | 124 |
\ No newline at end of file |
| 121 | 125 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,26 @@ |
| 1 |
+% Generated by roxygen2: do not edit by hand |
|
| 2 |
+% Please edit documentation in R/SCONE_DEFAULTS.R |
|
| 3 |
+\name{CLR_FN}
|
|
| 4 |
+\alias{CLR_FN}
|
|
| 5 |
+\title{Centered log-ratio (CLR) normalization wrapper function}
|
|
| 6 |
+\usage{
|
|
| 7 |
+CLR_FN(ei) |
|
| 8 |
+} |
|
| 9 |
+\arguments{
|
|
| 10 |
+\item{ei}{Numerical matrix. (rows = genes, cols = samples).}
|
|
| 11 |
+} |
|
| 12 |
+\value{
|
|
| 13 |
+CLR normalized matrix. |
|
| 14 |
+} |
|
| 15 |
+\description{
|
|
| 16 |
+Centered log-ratio (CLR) normalization wrapper function |
|
| 17 |
+} |
|
| 18 |
+\details{
|
|
| 19 |
+SCONE scaling wrapper for |
|
| 20 |
+ \code{\link[compositions]{clr}}).
|
|
| 21 |
+} |
|
| 22 |
+\examples{
|
|
| 23 |
+ei <- matrix(0:20,nrow = 7) |
|
| 24 |
+eo <- CLR_FN(ei) |
|
| 25 |
+ |
|
| 26 |
+} |
| ... | ... |
@@ -2,7 +2,7 @@ |
| 2 | 2 |
% Please edit documentation in R/SCONE_DEFAULTS.R |
| 3 | 3 |
\name{DESEQ_FN}
|
| 4 | 4 |
\alias{DESEQ_FN}
|
| 5 |
-\title{DESeq size factor scaling normalization wrapper function}
|
|
| 5 |
+\title{Relative log-expression (RLE; DESeq) scaling normalization wrapper function}
|
|
| 6 | 6 |
\usage{
|
| 7 | 7 |
DESEQ_FN(ei) |
| 8 | 8 |
} |
| ... | ... |
@@ -10,14 +10,13 @@ DESEQ_FN(ei) |
| 10 | 10 |
\item{ei}{Numerical matrix. (rows = genes, cols = samples).}
|
| 11 | 11 |
} |
| 12 | 12 |
\value{
|
| 13 |
-DESeq size factor normalized matrix. |
|
| 13 |
+RLE normalized matrix. |
|
| 14 | 14 |
} |
| 15 | 15 |
\description{
|
| 16 |
-DESeq size factor scaling normalization wrapper function |
|
| 16 |
+Relative log-expression (RLE; DESeq) scaling normalization wrapper function |
|
| 17 | 17 |
} |
| 18 | 18 |
\details{
|
| 19 |
-SCONE scaling wrapper for |
|
| 20 |
- \code{\link[DESeq]{estimateSizeFactorsForMatrix}}).
|
|
| 19 |
+SCONE scaling wrapper for \code{\link[edgeR]{calcNormFactors}}).
|
|
| 21 | 20 |
} |
| 22 | 21 |
\examples{
|
| 23 | 22 |
ei <- matrix(0:20,nrow = 7) |
| 24 | 23 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,25 @@ |
| 1 |
+% Generated by roxygen2: do not edit by hand |
|
| 2 |
+% Please edit documentation in R/SCONE_DEFAULTS.R |
|
| 3 |
+\name{SUM_FN}
|
|
| 4 |
+\alias{SUM_FN}
|
|
| 5 |
+\title{Sum scaling normalization function}
|
|
| 6 |
+\usage{
|
|
| 7 |
+SUM_FN(ei) |
|
| 8 |
+} |
|
| 9 |
+\arguments{
|
|
| 10 |
+\item{ei}{Numerical matrix. (rows = genes, cols = samples).}
|
|
| 11 |
+} |
|
| 12 |
+\value{
|
|
| 13 |
+Sum-scaled normalized matrix. |
|
| 14 |
+} |
|
| 15 |
+\description{
|
|
| 16 |
+Sum scaling normalization function |
|
| 17 |
+} |
|
| 18 |
+\details{
|
|
| 19 |
+SCONE scaling by library size or summed expression. |
|
| 20 |
+} |
|
| 21 |
+\examples{
|
|
| 22 |
+ei <- matrix(0:20,nrow = 7) |
|
| 23 |
+eo <- SUM_FN(ei) |
|
| 24 |
+ |
|
| 25 |
+} |
