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Beatrice Tan
CNAprioritization
Commits
125ef5d2
Commit
125ef5d2
authored
Feb 19, 2018
by
Beatrice Tan
Browse files
Removed scripts which are not used.
parent
c339d65e
Changes
2
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config_laptop.yaml
deleted
100644 → 0
View file @
c339d65e
#Directories to be specified
#workdir: /home/bftan/CNA_results #directory to write output
#gisticdir: /home/bftan/Tools/GISTIC2_test #directory to install GISTIC2
#workdir: /home/bftan/CNA_results #directory to write output
#gisticdir: /home/bftan/Tools/GISTIC2 #directory to install GISTIC2
workdir
:
/home/beatrice/CNA_analysis
gisticdir
:
/home/beatrice/CNA_analysis/run_gistic2
#Input details to download from firehose
cancer_type
:
SKCM
date_data
:
"
2016_07_15"
#Or provide input file
inputfile
:
"
"
#tumor segmentation data
normal
:
"
"
#normal segmentation data
#Data for running and benchmarking tools.
reference
:
hg19
prev_found_genes
:
input_files/intogen-CM-drivers-data.tsv
census_genes
:
input_files/Census_genes.txt
biomart_genes
:
input_files/biomart_human_genes.tsv
#Settings GISTIC2.0
gistic_precision
:
"
99"
settings_gistic
:
"
-ta
0.1
-td
0.1
-qvt
0.25
-brlen
0.7
-cap
1.5
-rx
1
-genegistic
1
-conf
0.99"
#Settings for sample size differences
sizes
:
[
20
,
30
,
40
,
50
,
60
,
70
,
80
,
90
]
#sizes: [30, 40]
repeats
:
[
1
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,
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,
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,
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]
scripts/plot_regions.R
deleted
100644 → 0
View file @
c339d65e
#!/usr/bin/env Rscript
args
=
commandArgs
(
trailingOnly
=
TRUE
)
source
(
"https://bioconductor.org/biocLite.R"
)
biocLite
(
"karyoploteR"
)
bed
=
read.table
(
args
[
1
],
sep
=
"\t"
,
header
=
TRUE
)
#Read output plot files?
#chrom as "chr1"
kp
<-
plotKaryotype
(
chromosomes
=
c
(
chrom
))
#kpDataBackground(kp)
kpAxis
(
kp
)
kpRect
(
kp
,
chr
=
chrom
,
x0
=
start
,
x1
=
end
,
y0
=
0.2
,
y1
=
0.4
)
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