1. structToolbox
  2. Commit 28789fb1df22c8a26e6d9a33ee14d625b91cb567
Browse code

add sbcms correction method

grlloyd authored on 16/07/2019 08:58:01
Showing 4 changed files
DESCRIPTION
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@@ -54,6 +54,7 @@ Collate:
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     'prop_na_class.R'
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     'r_squared_class.R'
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     'rsd_filter.R'
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+    'sb_corr.R'
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     'sbcms_dataset_class.R'
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     'split_data_class.R'
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     'structToolbox.R'
NAMESPACE
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@@ -76,6 +76,7 @@ export(prop_na)
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 export(r_squared)
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 export(rsd_filter)
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 export(rsd_filter.hist)
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+export(sb_corr)
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 export(sbcms_dataset)
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 export(split_data)
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 export(tSNE)
R/sb_corr.R
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+#' sbcms
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+#'
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+#' Signal/batch correction using SMCBMS package
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+#' @export sb_corr
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+#' @examples
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+#' M = sb_corr()
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+sb_corr<-setClass(
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+    "sb_corr",
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+    contains = c('method'),
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+    slots=c(
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+        params.order_col='entity',
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+        params.batch_col='entity',
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+        params.qc_col='entity',
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+        params.smooth='entity',
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+        params.use_log='entity',
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+        params.min_qc='entity',
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+        outputs.corrected='entity'
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+    ),
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+
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+    prototype=list(
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+        name = 'Signal/batch correction for mass spectrometry data',
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+        description = 'Applies Quality Control Robust Spline (QC-RSC) method to
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+        correct for signal drift and batch differences in mass spectrometry data.',
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+        type = 'correction',
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+        predicted = 'corrected',
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+
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+        params.order_col=entity(
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+            name = 'Sample run order column',
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+            description = 'The column name of sample_meta indicating the run order of the samples.',
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+            value = character(0),
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+            type='character'),
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+
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+        params.batch_col=entity(
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+            name = 'Batch ID column',
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+            description = 'The column name of sample_meta indicating the batch each sample was measured in.',
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+            value = character(0),
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+            type='character'),
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+
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+        params.qc_col=entity(
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+            name = 'Class ID column',
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+            description = 'The column name of sample_meta indicating the group each sample is a member of.',
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+            value = character(0),
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+            type='character'),
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+
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+        params.smooth=entity(
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+            name = 'Spline smoothing parameter',
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+            description = 'Should be in the range 0 to 1. If set to 0 (default) it will be estimated using
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+            leave-one-out cross-validation.',
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+            value = 0,
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+            type='numeric'),
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+
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+        params.use_log=entity(
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+            name = 'Use log transformed data',
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+            description = 'TRUE or FALSE to perform the signal correction fit on the log scaled data. Default is TRUE.',
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+            value = 0,
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+            type='numeric'),
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+
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+        params.min_qc=entity(
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+            name = 'Minimum number of QCs',
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+            description = 'Minimum number of QC samples required for signal correction.',
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+            value = 4,
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+            type='numeric'),
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+
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+        outputs.corrected=entity(name = 'Signal/batch corrected dataset',
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+            description = 'THe dataset after signal/batch correction has been applied.',
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+            type='dataset',
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+            value=dataset()
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+        )
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+    )
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+)
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+
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+#' @export
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+setMethod(f="method.apply",
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+    signature=c("sb_corr","dataset"),
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+    definition=function(M,D)
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+    {
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+        rn=rownames(D$data)
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+        cn=colnames(D$data)
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+        # uses transposed data
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+        X=as.data.frame(t(D$data))
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+
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+        # apply correction
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+        corrected_data <- sbcms::QCRSC(
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+            df=X,
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+            order=D$sample_meta[[M$order_col]],
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+            batch=D$sample_meta[[M$batch_col]],
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+            classes=D$sample_meta[[M$qc_col]],
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+            spar=M$smooth,
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+            minQC=M$min_qc,
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+            log=M$use_log
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+        )
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+
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+        D$data=as.data.frame(t(corrected_data))
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+        rownames(D$data)=rn
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+        colnames(D$data)=cn
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+
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+        M$corrected=D
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+        return(M)
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+    }
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+)
man/sb_corr-class.Rd
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/sb_corr.R
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+\docType{class}
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+\name{sb_corr-class}
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+\alias{sb_corr-class}
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+\alias{sb_corr}
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+\title{sbcms}
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+\description{
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+Signal/batch correction using SMCBMS package
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+}
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+\examples{
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+M = sb_corr()
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+}