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Commit 5ad8cc40 authored by Francesco Favero's avatar Francesco Favero Committed by Gabor Csardi
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version 2.1.2

parent 4547049a
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......@@ -4,8 +4,8 @@ Description: Tools to analyze genomic sequencing data from
paired normal-tumor samples, including cellularity and ploidy estimation; mutation
and copy number (allele-specific and total copy number) detection, quantification
and visualization.
Version: 2.1.1
Date: 2015-01-20
Version: 2.1.2
Date: 2015-08-18
Author: Francesco Favero, Andrea M. Marquard, Tejal Joshi, Aron C. Eklund
Maintainer: Francesco Favero <favero@cbs.dtu.dk>
Depends: R (>= 3.0.0), copynumber, parallel, squash
......@@ -13,7 +13,7 @@ Suggests:
License: GPL-3
URL: http://cbs.dtu.dk/biotools/sequenza/, Mailing list:
https://groups.google.com/forum/#!forum/sequenza-user-group
Packaged: 2015-01-20 04:38:23 UTC; favero
NeedsCompilation: no
Packaged: 2015-10-08 19:07:04 UTC; favero
Repository: CRAN
Date/Publication: 2015-01-27 16:55:55
Date/Publication: 2015-10-10 01:22:44
910f6c45e9e62ddf06de4d13bda4979e *DESCRIPTION
6d09bc56bb99e294c2ec6382e914b2fd *NAMESPACE
2006f46b799bcf41bd5236f6a78f801c *NEWS
281ba3b00e96742b07bd8da9b5901781 *DESCRIPTION
b5079032d430e0b0bb6b382850bab79e *NAMESPACE
f5d14f74caa7d1111a222462ea8c8019 *NEWS
aeda5901d16339bb5d61ee434422e86d *R/analysis.R
47d5566ca1686c3dabde59008b84f989 *R/bayes.R
592d7b6911d9d06e18b388eed8cbcea3 *R/graphics.R
d4080194f646974cb4f3c0089378f6de *R/misc.R
4020afb3d3685ecdc0ffa459ff213c2d *R/model.R
e52bd46020494d28003d6615c41d1c0e *R/next.R
cccf4b89f6441d5f4d0b81ef88bb46da *R/next.R
4c2d13a41cc82e15cdc73cd9d0c25e2a *R/workflows.R
dc22c9077dd9a1916c9062e69180a45e *build/vignette.rds
33cb86ef72ebdd33f91839241f0bd890 *data/CP.example.RData
f865934a3a177ac65318e881f0c0c3d3 *data/example.seqz.rda
0135dcde58f05c44f487ba7eea431d43 *build/vignette.rds
e867850542cfeaee96e0fe3b5701e396 *data/CP.example.RData
98b855b13711c56d6efb034e69530fa0 *data/example.seqz.rda
a13b971aa94a30d151176acb0bccf441 *data/example.seqz.txt.gz
473d6d18140e030b741d8e3685c271b3 *exec/sequenza-utils.py
49a67dbefc97a501bc47492ca1108e0a *inst/CITATION
e8a13df2363bce7b30d929083c7b40d7 *inst/doc/sequenza.R
4120d5d3657936c411c952be04c7f031 *inst/doc/sequenza.Rnw
4f7362a072270cae8a0ec89a2c59f342 *inst/doc/sequenza.pdf
1a6d89cde454972fe13fa738e7047618 *inst/doc/sequenza.pdf
a665959a09431961a03bfca5d9e6887c *man/CP.data.Rd
2443f587e9f9624836a0aece9d24acaf *man/VarScan2seqz.Rd
75446b25323a9826ec51350fee71236c *man/baf.bayes.Rd
......
......@@ -35,4 +35,48 @@ import(
squash
)
importFrom("grDevices",
"colorRampPalette",
"dev.off",
"gray.colors",
"heat.colors",
"palette",
"pdf",
"rgb"
)
importFrom("graphics",
"abline",
"axis",
"barplot",
"contour",
"legend",
"mtext",
"par",
"plot",
"points",
"polygon",
"rect",
"segments",
"strwidth",
"text"
)
importFrom("stats",
"dbinom",
"dpois",
"dt",
"median",
"na.exclude",
"quantile",
"sd",
"setNames",
"weighted.mean"
)
importFrom("utils",
"packageVersion",
"read.delim",
"read.table",
"setTxtProgressBar",
"tail",
"txtProgressBar",
"write.table"
)
Changes in version 2.1.2 (2015-08-18)
- Keep the order of the bases corresponding to the major and minor alleles as in the normal sample. (allows mocking haplotype).
- Fix check for NOTES in newer R versions
Changes in version 2.1.1 (2015-01-20)
- Fix heterozygous detection when importing VarScan2 data of very high coverage seq.
- Cleanup sequenza-utils.py
......
......@@ -75,7 +75,17 @@ VarScan2seqz <- function(varscan.somatic, varscan.copynumber = NULL, normal_var_
idx <- zygosity.normal == 'het' & Af < 0.5
Af[idx] <- 1 - Af[idx]
idx <- zygosity.normal == 'het'
Bf[idx] <- 1 - Af[idx]
Bf[idx] <- 1 - Af[idx]
## Overwrite the Genotype base orders to
## support pseudo haplotype analysis.
genotype_1 <- varscan.somatic[idx, c("ref", "var")]
genotype_1 <- apply(genotype_1, 1, paste, collapse = "")
AB.normal[idx] <- genotype_1
idx <- idx & varscan.somatic$tumor_var_freq > 0.5
genotype_2 <- varscan.somatic[idx, c("var", "ref")]
genotype_2 <- apply(genotype_2, 1, paste, collapse = "")
AB.normal[idx] <- genotype_2
## Not the best way, but I'm running out of ideas
idx <- zygosity.normal == 'hom' & varscan.somatic$somatic_status == 'Somatic'
if (sum(idx) > 0) {
mut.b <- cbind(as.character(iupac.nucs[varscan.somatic$tumor_gt[idx]]),
......
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