CGHcall

[…] er for regions of germline copy number variation. The results are provided in tab-separated format. The third function is optional and allows segmentation using CBS [] as implemented in the R-package CGHcall 2.22.0 [], and plotting of the results. Control-FREEC takes as an input aligned reads, then constructs and normalizes the copy number profile, constructs the BAF profile, segments both profile […]

[…] using the function “normalize.quantiles” from the “preprocessCore” R package. Genome segmentation was performed according to () using the “segment” function as implemented in the “DNAcopy” R package “CGHcall”. Segmentation and all subsequent steps were performed for each tumor type independently. For each comparison of interest, the ratio was computed between the sample and its corresponding contr […]

[…] and 1 μg reference genomic DNA male pool (G147A, Promega, Leiden, the Netherlands) labeled with ULS-Cy3 (Agilent Genomic DNA ULS Labeling Kit). Using median log ratios, data were normalized using the CGHcall version 2.14.0, centralized using CGHnormaliter version 1.8.0, and segmented and called using CGHcall default settings (−1 for loss, 0 for diploid, 1 for gain and 2 for amplification) in R ver […]

[…] LUAD tumor samples (see Table ). Each of the public datasets was first normalized, segmented and additionally underwent post-segmentation normalization using methods provided by Bioconductor package CGHcall (v2.22.0) []. All three datasets then underwent a “calling” process using the CGHcall method from the same package, converting the continuous log-ratios on each probe, to one of the three disc […]

[…] n were assigned to each of the 261801 SNPs using a two-level hierarchical mixture model which utilizes the breakpoint information from the CBS []. CN frequency plots were created using the R package ‘CGHcall’ [], plotting the percentage of patients with a particular aberration (CN gain, high gain, CN loss, homozygous deletion) across chromosomal positions.Modified Manhattan plots based on the func […]

[…] excluded from downstream analysis. Within the QDNAseq package, bins were segmented using the ‘Circular Binary Segmentation’ algorithm and significantly ‘amplified’ or ‘lost’ regions were called using CGHcall – regions were called in peripheral fluids independent of the calls from the corresponding TUR sample.We compared overall levels of copy number imbalance across the length of the genome in our […]