CGHcall

[…] version 1.12.0 was used. to compare the logr values of the copy numbers between samples a centralization step was performed, using the r package cghnormaliter version 1.28.0. data were called using cghcall version 2.36.0 default settings (−2 for double loss, −1 for loss, 0 for diploid, 1 for gain and 2 for amplification) in r version 3.3.3., mrna was extracted from total rna and amplified 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 […]

[…] 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 […]

[…] 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 […]

[…] performed using human methylation 450k data from the nch-eortc glioblastoma dataset (n=64; geo accession number gse60274) [] and acgh-244k from tcga (n=415) []. a mixture model using the r package cghcall was used for classification as detailed previously []. the spearman ‘rank’ correlation between two genes was calculated using level 3 rnaseq data from the tcga gbm dataset (n=107) [] […]

[…] 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 […]