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This dataset contains basic chromosomal information for UCSC Human Genome Assembly July 2003 freeze.
● Data Source:
BioConductor
● Keywords: datasets
● Alias: chrominfo.Mb
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0 images
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convert.output
(Package: snapCGH) :
Converts the output from the simulation to a format which can be used by segmentation schemes available within R
This function converts the output obtained by applying our simulation scheme into a format that can be used (either directly or indirectly) as the input to various segmentation schemes available within R. Additionally, we are in the process of submitting a library to CRAN which will enable the user to apply a number of the segmentation schemes available within R to datasets which have the same structure as that generated by this function.
● Data Source:
BioConductor
● Keywords: datasets
● Alias: convert.output
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0 images
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log2ratios
(Package: snapCGH) :
Extracting log2 ratios
This function extracts the log2 ratios from either an MAList object or a SegList object.
● Data Source:
BioConductor
● Keywords: datasets
● Alias: log2ratios
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0 images
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non.zero.length.distr.non.tiled
(Package: snapCGH) :
Empirical distribution of segment lengths in non-tiled regions with copy number gains or losses
This file contains the empirical distribution of segment lengths (of untiled regions and whose state mean indicates that they correspond to regions of copy number gain or loss) derived by applying the DNAcopy segmentation scheme (Olshen et al., 2004) to an unpublished breast cancer dataset. Instead of using the physical length of the segments we calculate the lengths as a proportion of the length of the untiled region.
● Data Source:
BioConductor
● Keywords: datasets
● Alias: non.zero.length.distr.non.tiled
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0 images
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non.zero.length.distr.tiled
(Package: snapCGH) :
Empirical distribution of segment lengths in tiled regions with copy number gains or losses
This file contains the empirical distribution of segment lengths (of tiled regions and whose state mean indicates that they correspond to regions of copy number gain or loss) derived by applying the DNAcopy segmentation scheme (Olshen et al., 2004) to an unpublished breast cancer dataset. Instead of using the physical length of the segments we calculate the lengths as a proportion of the length of the tiled region.
● Data Source:
BioConductor
● Keywords: datasets
● Alias: non.zero.length.distr.tiled
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0 images
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simulateData
(Package: snapCGH) :
A function for simulating aCGH data and the corresponding clone layout
This simulation scheme operates in two stages. Initially, we simulate the layout of clones before using a modified version of the scheme developed by Willenbrock et al., 2005 to generate the log_2 ratios. For each simulated clone layout we generate 20 sets of simulated log_2 ratios from one of five templates. Additionally, we also take account of the cellularity of the test sample in our simulation.
● Data Source:
BioConductor
● Keywords: datasets
● Alias: generate.data, simulateData
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0 images
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zero.length.distr.non.tiled
(Package: snapCGH) :
Empirical distribution of segment lengths in non-tiled regions with no copy number gains or losses
This file contains the empirical distribution of segment lengths (of untiled regions and whose state mean indicates that they correspond to regions of no copy number gain or loss) derived by applying the DNAcopy segmentation scheme (Olshen et al., 2004) to an unpublished breast cancer dataset. Instead of using the physical length of the segments we calculate the lengths as a proportion of the length of the untiled region.
● Data Source:
BioConductor
● Keywords: datasets
● Alias: zero.length.distr.non.tiled
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0 images
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zero.length.distr.tiled
(Package: snapCGH) :
Empirical distribution of segment lengths in tiled regions with no copy number gains or losses
This file contains the empirical distribution of segment lengths (of tiled regions and whose state mean indicates that they correspond to regions of no copy number gain or loss) derived by applying the DNAcopy segmentation scheme (Olshen et al., 2004) to an unpublished breast cancer dataset. Instead of using the physical length of the segments we calculate the lengths as a proportion of the length of the tiled region.
● Data Source:
BioConductor
● Keywords: datasets
● Alias: zero.length.distr.tiled
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0 images
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