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

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

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

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)

ISSN: 1471-2105