Mercurial > repos > galaxyp > cardinal_preprocessing

comparison macros.xml @ 10:5abc3ab4792c draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ca89f8e007c6b17f7c30066729e05b8686ab975a"
author galaxyp
date Sun, 27 Sep 2020 11:10:30 +0000
parents ca727a6dede6
children accf9fb6ea01
comparison
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9:ca727a6dede6 10:5abc3ab4792c
115 ]]></token> 115 ]]></token>
116 116
117 <token name="@DATA_PROPERTIES_INRAM@"><![CDATA[ 117 <token name="@DATA_PROPERTIES_INRAM@"><![CDATA[
118 ########################### QC numbers ######################## 118 ########################### QC numbers ########################
119 ## including intensity calculations which need data in RAM 119 ## including intensity calculations which need data in RAM
120
121 int_matrix = as.matrix(spectra(msidata)) ## only load once into RAM, then re-use
122 ## Number of NA in spectra matrix
123 NAcount = sum(is.na(int_matrix))
124 ## replace NA with zero to calculate data properties based on intensity matrix, no change in msidata
125 int_matrix[is.na(int_matrix)] <- 0
126
120 ## Number of features (mz) 127 ## Number of features (mz)
121 maxfeatures = length(features(msidata)) 128 maxfeatures = length(features(msidata))
122 ## Range mz 129 ## Range mz
123 minmz = round(min(mz(msidata)), digits=2) 130 minmz = round(min(mz(msidata)), digits=2)
124 maxmz = round(max(mz(msidata)), digits=2) 131 maxmz = round(max(mz(msidata)), digits=2)
129 maximumx = max(coord(msidata)[,1]) 136 maximumx = max(coord(msidata)[,1])
130 ## Range y coordinates 137 ## Range y coordinates
131 minimumy = min(coord(msidata)[,2]) 138 minimumy = min(coord(msidata)[,2])
132 maximumy = max(coord(msidata)[,2]) 139 maximumy = max(coord(msidata)[,2])
133 ## Range of intensities 140 ## Range of intensities
134 minint = round(min(as.matrix(spectra(msidata)), na.rm=TRUE), digits=2) 141 minint = round(min(int_matrix), digits=2)
135 maxint = round(max(as.matrix(spectra(msidata)), na.rm=TRUE), digits=2) 142 maxint = round(max(int_matrix), digits=2)
136 ## Number of intensities > 0, for if conditions 143 ## Number of intensities > 0, for if conditions
137 npeaks= sum(as.matrix(spectra(msidata))>0, na.rm=TRUE) 144 npeaks= sum(int_matrix>0)
138 ## Number of NA in spectra matrix 145 ## Number of NA in spectra matrix
139 NAcount = sum(is.na(spectra(msidata))) 146 infcount = sum(is.infinite(int_matrix))
140 ## Number of NA in spectra matrix
141 infcount = sum(is.infinite(as.matrix(spectra(msidata))))
142 ## Number of duplicated coordinates 147 ## Number of duplicated coordinates
143 dupl_coord = sum(duplicated(coord(msidata))) 148 dupl_coord = sum(duplicated(coord(msidata)))
144 properties = c("Number of m/z features", 149 properties = c("Number of m/z features",
145 "Range of m/z values", 150 "Range of m/z values",
146 "Number of pixels", 151 "Number of pixels",