data: hg38_grangeslist

In navinlabcode/copykit: CopyKit

hg38_grangeslist

Description

hg38_grangeslist

hg19_rg

copykit_obj_rle

copykit_obj_filt_rle

copykit_obj_filt_umap

hg19_genes

hg38_genes

CopyKit Example

CopyKit Example

mock_bincounts

Usage

hg38_grangeslist

hg38_grangeslist

copykit_obj_filt_rle

copykit_obj_rle

copykit_obj_filt_umap

hg19_genes

hg38_genes

copykit_example()

copykit_example_filtered()

mock_bincounts(
  ncells = 30,
  ncells_diploid = 5,
  position_gain = 4900:5493,
  position_del = 6523:7056,
  genome = "hg38",
  resolution = "220kb",
  run_vst = TRUE,
  run_segmentation = TRUE,
  run_lognorm = TRUE
)

Arguments

ncells	A numeric with the total number of cells to simulate.
ncells_diploid	A numeric with the number of diploid cells to simulate
position_gain	A vector with the index of the bin counts in which chromosomal gains will be added.
position_del	A vector with the index of the bin counts in which chromosomal deletions will be placed.
genome	The assembly genome information to add to the metadata.
resolution	The resolution of the scaffold to add to the object metadata

Format

An object of class CompressedGRangesList of length 8.

An object of class CompressedGRangesList of length 8.

An object of class list of length 790.

An object of class list of length 1502.

An object of class matrix (inherits from array) with 790 rows and 2 columns.

An object of class GRanges of length 23056.

An object of class GRanges of length 30909.

Details

Contains a Rle object with the segment ratios values of the copykit BL1 example dataset. It is used by the functions copykit_example

Contains a Rle object with the segment ratios values of the copykit BL1 example filtered dataset. It is used by the functions copykit_example_filtered()

Contains the umap reduced dimension for the BL1 dataset as generated for the CopyKit manuscript

Contains the GrangesObject for the genomic positions of genes in the hg19 genome assembly

Contains the GrangesObject for the genomic positions of genes in the hg38 genome assembly

This function is largely used for examples of CopyKit functions.

This function returns a CopyKit object with the unfiltered dataset of the sample BL1. This sample was processed with ACT and is a liver metastasis from a primary breast cancer patient.

The CopyKit object contain only the segment ratio mean of each single cell and, therefore, is not compatible with the functions from the runVarbin module.

This function is largely used for examples of CopyKit functions.

This function returns a CopyKit object with the unfiltered dataset of the sample BL1. This sample was processed with ACT and is a liver metastasis from a primary breast cancer patient.

The CopyKit object contain only the segment ratio mean of each single cell and, therefore, is not compatible with the functions from the runVarbin module.

Value

Contains a GrangesList object with the scaffolds for each of the resolutions used by runVarbin, runCountReads and runSegmentation on the hg38 genome assembly.

Contains a GrangesList object with the scaffolds for each of the resolutions used by runVarbin, runCountReads and runSegmentation on the hg19 genome assembly.

A CopyKit object with data from BL1 sample from the CopyKit manuscript.

A CopyKit object with data from BL1 sample from the CopyKit manuscript with diploid and noise cells removed.

A CopyKit object with simulated bincounts

Source

library(TxDb.Hsapiens.UCSC.hg19.knownGene)

library(TxDb.Hsapiens.UCSC.hg38.knownGene)

navinlabcode/copykit documentation built on Sept. 22, 2023, 9:16 a.m.