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Table 3 Results of analyzing Dataset A with aff2sv and R-GADA

From: affy2sv: an R package to pre-process Affymetrix CytoScan HD and 750K arrays for SNP, CNV, inversion and mosaicism calling

IniProbe EndProbe LenProbe MeanAmp CHR State Sample
66690197 71078462 183 0.953 3 −1 1F549
94236184 117023549 447 0.237 X −1 1J014
52942 15383670 602 0.086 17 −1 1J567
17309881 21217575 121 0.132 22 1 1K397
17309881 21421319 127 0.377 22 −1 2A419
143559 15049329 495 0.890 18 −1 2B595
17309881 21364849 124 0.185 22 1 2D325
65997819 69181942 80 0.049 4 −1 2F584
22759438 32409066 444 0.130 15 −1 2G029
17309881 20192331 109 0.362 22 −1 2G159
83885323 86767689 117 0.265 7 1 2H598
4723882 27966028 709 1.055 5 −1 2L046
143559 11602053 416 0.072 18 −1 2L217
22759438 32409066 444 0.172 15 −1 3A913
12585825 23193309 337 0.837 8 −1 3B558
218476969 249191732 1144 0.070 1 −1 3C103
144131822 159100528 652 0.971 7 −1 8D582
134476 18433821 591 0.466 20 1 8D582
15529890 21862551 208 0.367 8 1 P609
  1. CNVs detected by R-GADA (T = 7, MinSegLen = 100) on the 315 .CEL files from Afymetrix CytoScan HD corresponding to the population diagnosed with intellectual disability (ID) in Dataset B. The table is the result of the exportation of the object created by R-GADA. The columns IniProbe, EndProbe, chromosome and LenProbe tells us how many probes are contained din the region detected as CNV event, the column sample shows the sample's name containing the CNV. The value given by MeanAmp is used to try to classify the event (in gain or loss), the result of this classification is seen in State (1: gain; −1: loss)