[DESIGN] # Design description author Sylvain Mareschal purpose GCB-ABC classification model, as published in JMD (PMID: 25891505) MLPA 1.9.1 updated 2016-05-15 [MLPA.process] # Arguments to be passed to the R function, see the Reference Manual for further details [read.fsa] # Arguments to be passed to the R function, see the Reference Manual for further details [align.fsa] # Arguments to be passed to the R function, see the Reference Manual for further details channel ROX outThreshold 0.4 maskOffScale FALSE [peaks.fsa] # Arguments to be passed to the R function, see the Reference Manual for further details logTransform TRUE lowThreshold 400 [plot.fsa] # Arguments to be passed to the R function, see the Reference Manual for further details channels ROX 6-FAM chanColors grey black xlim 80 123 ylim NA [model] # Arguments to be passed to the R function, see the Reference Manual for further details threshold 0.95 groupNames ABC GCB groupColors darkblue darkorange2 groupMeans 10.21696 -35.92091 groupSDs 7.51672 15.8074 geneNames LMO2 NEK6 MYBL1 TNFRSF13B BCL6 IRF4 IGHM FOXP1 geneTs -11.11728 -6.07617 -4.86899 4.4753 -3.59697 4.82121 4.51134 2.69062 geneMs 0.68433 0.38955 0.31225 0.46633 0.48262 1.48637 1.70233 1.35262 [classify] # Arguments to be passed to the R function, see the Reference Manual for further details plot TRUE [PEAKS] # Intervals in which look for a gene-related signal name channel size.min size.max color NEK6 6-FAM 82.5 83.5 darkorange2 IRF4 6-FAM 86.2 87.5 darkblue IGHM 6-FAM 90.5 92 darkblue CCND1 6-FAM 93.5 95 darkgrey LMO2 6-FAM 96 97.5 darkorange2 FOXP1 6-FAM 99 100.2 darkblue TNFRSF9 6-FAM 102.5 104 darkgrey BCL6 6-FAM 104.5 105.5 darkorange2 TNFRSF13B 6-FAM 106.5 107.5 darkblue CCND2 6-FAM 109 110 darkgrey MYC 6-FAM 111.5 112.5 darkgrey MYBL1 6-FAM 114.5 116 darkorange2 BCL2 6-FAM 118 119 darkgrey MS4A1 6-FAM 121 122.3 darkgreen