CLONETv2-package: CLONETv2
In CLONETv2: Clonality Estimates in Tumor
Description
Author(s)
References
Examples
Description
This package is designed to analyze data from next-generation sequencing
experiments on genomic samples. It offers a
set of functions to compute allele specific copy number and
clonality from segmented data and SNPs position pileup. The library
also calculated the clonality of single nucleotide variants given
read counts at mutated positions.
The package has been developed at the laboratory of Computational and Functional Oncology,
Department of CIBIO, University of Trento (Italy), under the supervision of prof.
Francesca Demichelis.
Author(s)
Maintainer:
Davide Prandi
Contributors:
Tarcisio Fedrizzi, Alessandro Romanel
References
Prandi, D., Baca, S. C., Romanel, A., Barbieri, C. E., Mosquera, J. M., Fontugne, J., Beltran,
H., Sboner,
A., Garraway, L. A., Rubin, M. A., and Demichelis, F. (2014). Unraveling the clonal hierarchy of
somatic genomic aberrations. Genome biology 15, 439.
Carreira, S., Romanel, A., Goodall, J., Grist, E., Ferraldeschi, R., Miranda, S., Prandi, D.,
Lorente, D.,
Frenel, J. S., Pezaro, C., et al. (2014). Tumor clone dynamics in lethal prostate cancer. Science
translational medicine 6, 254ra125.
Beltran, H., Eng, K., Mosquera, J. M., Sigaras, A., Romanel, A., Rennert, H., Kossai, M.,
Pauli, C.,
Faltas, B., Fontugne, J., et al. (2015). Whole-Exome Sequencing of Metastatic Cancer and
Biomarkers
of Treatment Response. JAMA Oncol 1, 466-474.
Faltas, B. M., Prandi, D., Tagawa, S. T., Molina, A. M., Nanus, D. M., Sternberg, C.,
Rosenberg, J.,
Mosquera, J. M., Robinson, B., Elemento, O., et al. (2016). Clonal evolution of
chemotherapyresistant
urothelial carcinoma. Nature genetics 48, 1490-1499.
Examples
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###############
###############
## Diploid tumor sample
## Load example data
seg_tb <- read.table(system.file("sample1.seg", package = "CLONETv2"),header = TRUE, as.is=TRUE)
pileup_tumor <- read.table(
gzfile(system.file("sample1_tumor_pileup.tsv.gz", package = "CLONETv2")),
header = TRUE, as.is=TRUE)
pileup_normal <- read.table(
gzfile(system.file("sample1_normal_pileup.tsv.gz", package = "CLONETv2")),
header = TRUE, as.is=TRUE)
snv_reads <- read.table(system.file("sample1_snv_read_count.tsv", package = "CLONETv2"),
header = TRUE, as.is=TRUE, comment.char = "", check.names = FALSE, na.strings = "-")
## Compute beta table with default parameters
bt <- compute_beta_table(seg_tb, pileup_tumor, pileup_normal)
## Compute ploidy table with default parameters
pl_table <- compute_ploidy(bt)
## Compute admixture table with default parameters (admixture= 1-tumor_purity)
adm_table <- compute_dna_admixture(beta_table = bt, ploidy_table = pl_table)
## Check ploidy and admixture estimates
check_plot <- check_ploidy_and_admixture(beta_table = bt, ploidy_table = pl_table,
admixture_table = adm_table)
print(check_plot)
## Compute clonality table with default parameters
scna_clonality_table <- compute_scna_clonality_table(beta_table = bt, ploidy_table = pl_table,
admixture_table = adm_table)
## Compute allele specific scna
allele_specific_cna_table <- compute_allele_specific_scna_table(beta_table = bt,
ploidy_table = pl_table, admixture_table = adm_table)
## Compute snvs colonality
sample_id <- "sample1"
snv_clonality_table <- compute_snv_clonality(sample_id = sample_id, snv_read_count = snv_reads,
beta_table = bt, ploidy_table = pl_table, admixture_table = adm_table)
###############
###############
## Aneuploid tumor sample
## Load example data
seg_tb <- read.table(system.file("sample2.seg", package = "CLONETv2"),header = TRUE, as.is=TRUE)
pileup_tumor <- read.table(
gzfile(system.file("sample2_tumor_pileup.tsv.gz", package = "CLONETv2")),
header = TRUE, as.is=TRUE)
pileup_normal <- read.table(
gzfile(system.file("sample2_normal_pileup.tsv.gz", package = "CLONETv2")),
header = TRUE, as.is=TRUE)
snv_reads <- read.table(system.file("sample2_snv_read_count.tsv", package = "CLONETv2"),
header = TRUE, as.is=TRUE, comment.char = "", check.names = FALSE, na.strings = "-")
## Compute beta table with default parameters
bt <- compute_beta_table(seg_tb, pileup_tumor, pileup_normal)
## Compute ploidy table with default parameters
pl_table <- compute_ploidy(bt)
## Compute admixture table with default parameters (admixture= 1-tumor_purity)
adm_table <- compute_dna_admixture(beta_table = bt, ploidy_table = pl_table)
## Check ploidy and admixture estimates
check_plot <- check_ploidy_and_admixture(beta_table = bt, ploidy_table = pl_table,
admixture_table = adm_table)
print(check_plot)
## Compute clonality table with default parameters
scna_clonality_table <- compute_scna_clonality_table(beta_table = bt, ploidy_table = pl_table,
admixture_table = adm_table)
## Compute allele specific scna
allele_specific_cna_table <- compute_allele_specific_scna_table(beta_table = bt,
ploidy_table = pl_table, admixture_table = adm_table)
## Compute snvs colonality
sample_id <- "sample2"
snv_clonality_table <- compute_snv_clonality(sample_id = sample_id, snv_read_count = snv_reads,
beta_table = bt, ploidy_table = pl_table, admixture_table = adm_table)
###############
###############
## Aneuploidy tumor sample with problematic ploidy estimate
## Load example data
seg_tb <- read.table(system.file("sample3.seg", package = "CLONETv2"),header = TRUE, as.is=TRUE)
pileup_tumor <- read.table(
gzfile(system.file("sample3_tumor_pileup.tsv.gz", package = "CLONETv2")),
header = TRUE, as.is=TRUE)
pileup_normal <- read.table(
gzfile(system.file("sample3_normal_pileup.tsv.gz", package = "CLONETv2")),
header = TRUE, as.is=TRUE)
## Compute beta table with default parameters
bt <- compute_beta_table(seg_tb, pileup_tumor, pileup_normal)
## Compute ploidy table with default parameters
pl_table <- compute_ploidy(bt)
## Compute admixture table with default parameters (admixture= 1-tumor_purity)
adm_table <- compute_dna_admixture(beta_table = bt, ploidy_table = pl_table)
## Check ploidy and admixture estimates
check_plot <- check_ploidy_and_admixture(beta_table = bt, ploidy_table = pl_table,
admixture_table = adm_table)
print(check_plot)
## Observed data (gray points) does not fit with expcted positions (Red circles)
###############
###############
## Tumor sample with problem in the segmented input data
## Load example data
seg_tb <- read.table(system.file("sample4.seg", package = "CLONETv2"),header = TRUE, as.is=TRUE)
pileup_tumor <- read.table(
gzfile(system.file("sample4_tumor_pileup.tsv.gz", package = "CLONETv2")),
header = TRUE, as.is=TRUE)
pileup_normal <- read.table(
gzfile(system.file("sample4_normal_pileup.tsv.gz", package = "CLONETv2")),
header = TRUE, as.is=TRUE)
## Compute beta table with default parameters
bt <- compute_beta_table(seg_tb, pileup_tumor, pileup_normal)
## Compute ploidy table with default parameters
pl_table <- compute_ploidy(bt)
## Compute admixture table with default parameters (admixture= 1-tumor_purity)
adm_table <- compute_dna_admixture(beta_table = bt, ploidy_table = pl_table)
## Check ploidy and admixture estimates
check_plot <- check_ploidy_and_admixture(beta_table = bt, ploidy_table = pl_table,
admixture_table = adm_table)
print(check_plot)
## CLONETv2 does not provide an estimate of the DNA admixture because
## (LogR, beta) data does not fit any CLONETv2 model
###############
###############
## Diploid tumor sample with subclonal hemizygous and homozygous deletions
## Load example data
seg_tb <- read.table(system.file("sample5.seg", package = "CLONETv2"),header = TRUE, as.is=TRUE)
pileup_tumor <- read.table(
gzfile(system.file("sample5_tumor_pileup.tsv.gz", package = "CLONETv2")),
header = TRUE, as.is=TRUE)
pileup_normal <- read.table(
gzfile(system.file("sample5_normal_pileup.tsv.gz", package = "CLONETv2")),
header = TRUE, as.is=TRUE)
snv_reads <- read.table(system.file("sample5_snv_read_count.tsv", package = "CLONETv2"),
header = TRUE, as.is=TRUE, comment.char = "", check.names = FALSE, na.strings = "-")
## Compute beta table with default parameters
bt <- compute_beta_table(seg_tb, pileup_tumor, pileup_normal)
## Compute ploidy table with default parameters
pl_table <- compute_ploidy(bt)
## Compute admixture table with default parameters (admixture= 1-tumor_purity)
adm_table <- compute_dna_admixture(beta_table = bt, ploidy_table = pl_table)
## Check ploidy and admixture estimates
check_plot <- check_ploidy_and_admixture(beta_table = bt, ploidy_table = pl_table,
admixture_table = adm_table)
print(check_plot)
## Compute clonality table with default parameters
scna_clonality_table <- compute_scna_clonality_table(beta_table = bt, ploidy_table = pl_table,
admixture_table = adm_table)
## Compute allele specific scna
allele_specific_cna_table <- compute_allele_specific_scna_table(beta_table = bt,
ploidy_table = pl_table, admixture_table = adm_table)
## Compute snvs colonality
sample_id <- "sample5"
snv_clonality_table <- compute_snv_clonality(sample_id = sample_id, snv_read_count = snv_reads,
beta_table = bt, ploidy_table = pl_table, admixture_table = adm_table)
CLONETv2 documentation built on Oct. 14, 2021, 1:07 a.m.
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Description Author(s) References Examples
Description
This package is designed to analyze data from next-generation sequencing experiments on genomic samples. It offers a set of functions to compute allele specific copy number and clonality from segmented data and SNPs position pileup. The library also calculated the clonality of single nucleotide variants given read counts at mutated positions.
The package has been developed at the laboratory of Computational and Functional Oncology, Department of CIBIO, University of Trento (Italy), under the supervision of prof. Francesca Demichelis.
Author(s)
Maintainer: Davide Prandi
Contributors: Tarcisio Fedrizzi, Alessandro Romanel
References
Prandi, D., Baca, S. C., Romanel, A., Barbieri, C. E., Mosquera, J. M., Fontugne, J., Beltran, H., Sboner, A., Garraway, L. A., Rubin, M. A., and Demichelis, F. (2014). Unraveling the clonal hierarchy of somatic genomic aberrations. Genome biology 15, 439.
Carreira, S., Romanel, A., Goodall, J., Grist, E., Ferraldeschi, R., Miranda, S., Prandi, D., Lorente, D., Frenel, J. S., Pezaro, C., et al. (2014). Tumor clone dynamics in lethal prostate cancer. Science translational medicine 6, 254ra125.
Beltran, H., Eng, K., Mosquera, J. M., Sigaras, A., Romanel, A., Rennert, H., Kossai, M., Pauli, C., Faltas, B., Fontugne, J., et al. (2015). Whole-Exome Sequencing of Metastatic Cancer and Biomarkers of Treatment Response. JAMA Oncol 1, 466-474.
Faltas, B. M., Prandi, D., Tagawa, S. T., Molina, A. M., Nanus, D. M., Sternberg, C., Rosenberg, J., Mosquera, J. M., Robinson, B., Elemento, O., et al. (2016). Clonal evolution of chemotherapyresistant urothelial carcinoma. Nature genetics 48, 1490-1499.
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 | ###############
###############
## Diploid tumor sample
## Load example data
seg_tb <- read.table(system.file("sample1.seg", package = "CLONETv2"),header = TRUE, as.is=TRUE)
pileup_tumor <- read.table(
gzfile(system.file("sample1_tumor_pileup.tsv.gz", package = "CLONETv2")),
header = TRUE, as.is=TRUE)
pileup_normal <- read.table(
gzfile(system.file("sample1_normal_pileup.tsv.gz", package = "CLONETv2")),
header = TRUE, as.is=TRUE)
snv_reads <- read.table(system.file("sample1_snv_read_count.tsv", package = "CLONETv2"),
header = TRUE, as.is=TRUE, comment.char = "", check.names = FALSE, na.strings = "-")
## Compute beta table with default parameters
bt <- compute_beta_table(seg_tb, pileup_tumor, pileup_normal)
## Compute ploidy table with default parameters
pl_table <- compute_ploidy(bt)
## Compute admixture table with default parameters (admixture= 1-tumor_purity)
adm_table <- compute_dna_admixture(beta_table = bt, ploidy_table = pl_table)
## Check ploidy and admixture estimates
check_plot <- check_ploidy_and_admixture(beta_table = bt, ploidy_table = pl_table,
admixture_table = adm_table)
print(check_plot)
## Compute clonality table with default parameters
scna_clonality_table <- compute_scna_clonality_table(beta_table = bt, ploidy_table = pl_table,
admixture_table = adm_table)
## Compute allele specific scna
allele_specific_cna_table <- compute_allele_specific_scna_table(beta_table = bt,
ploidy_table = pl_table, admixture_table = adm_table)
## Compute snvs colonality
sample_id <- "sample1"
snv_clonality_table <- compute_snv_clonality(sample_id = sample_id, snv_read_count = snv_reads,
beta_table = bt, ploidy_table = pl_table, admixture_table = adm_table)
###############
###############
## Aneuploid tumor sample
## Load example data
seg_tb <- read.table(system.file("sample2.seg", package = "CLONETv2"),header = TRUE, as.is=TRUE)
pileup_tumor <- read.table(
gzfile(system.file("sample2_tumor_pileup.tsv.gz", package = "CLONETv2")),
header = TRUE, as.is=TRUE)
pileup_normal <- read.table(
gzfile(system.file("sample2_normal_pileup.tsv.gz", package = "CLONETv2")),
header = TRUE, as.is=TRUE)
snv_reads <- read.table(system.file("sample2_snv_read_count.tsv", package = "CLONETv2"),
header = TRUE, as.is=TRUE, comment.char = "", check.names = FALSE, na.strings = "-")
## Compute beta table with default parameters
bt <- compute_beta_table(seg_tb, pileup_tumor, pileup_normal)
## Compute ploidy table with default parameters
pl_table <- compute_ploidy(bt)
## Compute admixture table with default parameters (admixture= 1-tumor_purity)
adm_table <- compute_dna_admixture(beta_table = bt, ploidy_table = pl_table)
## Check ploidy and admixture estimates
check_plot <- check_ploidy_and_admixture(beta_table = bt, ploidy_table = pl_table,
admixture_table = adm_table)
print(check_plot)
## Compute clonality table with default parameters
scna_clonality_table <- compute_scna_clonality_table(beta_table = bt, ploidy_table = pl_table,
admixture_table = adm_table)
## Compute allele specific scna
allele_specific_cna_table <- compute_allele_specific_scna_table(beta_table = bt,
ploidy_table = pl_table, admixture_table = adm_table)
## Compute snvs colonality
sample_id <- "sample2"
snv_clonality_table <- compute_snv_clonality(sample_id = sample_id, snv_read_count = snv_reads,
beta_table = bt, ploidy_table = pl_table, admixture_table = adm_table)
###############
###############
## Aneuploidy tumor sample with problematic ploidy estimate
## Load example data
seg_tb <- read.table(system.file("sample3.seg", package = "CLONETv2"),header = TRUE, as.is=TRUE)
pileup_tumor <- read.table(
gzfile(system.file("sample3_tumor_pileup.tsv.gz", package = "CLONETv2")),
header = TRUE, as.is=TRUE)
pileup_normal <- read.table(
gzfile(system.file("sample3_normal_pileup.tsv.gz", package = "CLONETv2")),
header = TRUE, as.is=TRUE)
## Compute beta table with default parameters
bt <- compute_beta_table(seg_tb, pileup_tumor, pileup_normal)
## Compute ploidy table with default parameters
pl_table <- compute_ploidy(bt)
## Compute admixture table with default parameters (admixture= 1-tumor_purity)
adm_table <- compute_dna_admixture(beta_table = bt, ploidy_table = pl_table)
## Check ploidy and admixture estimates
check_plot <- check_ploidy_and_admixture(beta_table = bt, ploidy_table = pl_table,
admixture_table = adm_table)
print(check_plot)
## Observed data (gray points) does not fit with expcted positions (Red circles)
###############
###############
## Tumor sample with problem in the segmented input data
## Load example data
seg_tb <- read.table(system.file("sample4.seg", package = "CLONETv2"),header = TRUE, as.is=TRUE)
pileup_tumor <- read.table(
gzfile(system.file("sample4_tumor_pileup.tsv.gz", package = "CLONETv2")),
header = TRUE, as.is=TRUE)
pileup_normal <- read.table(
gzfile(system.file("sample4_normal_pileup.tsv.gz", package = "CLONETv2")),
header = TRUE, as.is=TRUE)
## Compute beta table with default parameters
bt <- compute_beta_table(seg_tb, pileup_tumor, pileup_normal)
## Compute ploidy table with default parameters
pl_table <- compute_ploidy(bt)
## Compute admixture table with default parameters (admixture= 1-tumor_purity)
adm_table <- compute_dna_admixture(beta_table = bt, ploidy_table = pl_table)
## Check ploidy and admixture estimates
check_plot <- check_ploidy_and_admixture(beta_table = bt, ploidy_table = pl_table,
admixture_table = adm_table)
print(check_plot)
## CLONETv2 does not provide an estimate of the DNA admixture because
## (LogR, beta) data does not fit any CLONETv2 model
###############
###############
## Diploid tumor sample with subclonal hemizygous and homozygous deletions
## Load example data
seg_tb <- read.table(system.file("sample5.seg", package = "CLONETv2"),header = TRUE, as.is=TRUE)
pileup_tumor <- read.table(
gzfile(system.file("sample5_tumor_pileup.tsv.gz", package = "CLONETv2")),
header = TRUE, as.is=TRUE)
pileup_normal <- read.table(
gzfile(system.file("sample5_normal_pileup.tsv.gz", package = "CLONETv2")),
header = TRUE, as.is=TRUE)
snv_reads <- read.table(system.file("sample5_snv_read_count.tsv", package = "CLONETv2"),
header = TRUE, as.is=TRUE, comment.char = "", check.names = FALSE, na.strings = "-")
## Compute beta table with default parameters
bt <- compute_beta_table(seg_tb, pileup_tumor, pileup_normal)
## Compute ploidy table with default parameters
pl_table <- compute_ploidy(bt)
## Compute admixture table with default parameters (admixture= 1-tumor_purity)
adm_table <- compute_dna_admixture(beta_table = bt, ploidy_table = pl_table)
## Check ploidy and admixture estimates
check_plot <- check_ploidy_and_admixture(beta_table = bt, ploidy_table = pl_table,
admixture_table = adm_table)
print(check_plot)
## Compute clonality table with default parameters
scna_clonality_table <- compute_scna_clonality_table(beta_table = bt, ploidy_table = pl_table,
admixture_table = adm_table)
## Compute allele specific scna
allele_specific_cna_table <- compute_allele_specific_scna_table(beta_table = bt,
ploidy_table = pl_table, admixture_table = adm_table)
## Compute snvs colonality
sample_id <- "sample5"
snv_clonality_table <- compute_snv_clonality(sample_id = sample_id, snv_read_count = snv_reads,
beta_table = bt, ploidy_table = pl_table, admixture_table = adm_table)
|
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