plot_lrr_maf: CNV raw data plot
In SinomeM/cnv_geaRs: A little gear kit to manage CNV calling results
Description
Usage
Arguments
Details
Value
Author(s)
Description
lrr_plot create scatter plots of LRR and MAF
in a selected region
Usage
1
2
plot_lrr_maf(chr, cnv.start, cnv.end, region = 5, final.rep,
window = 100, step = 50)
Arguments
chr
Chromosome where the putative CNV is present (e.g "1", not "chr1")
cnv.start
Start position of the CNV
cnv.end
End position of the CNV
region
Size of the region to be plotted on each side of the CNV
final.rep
Data frame in Illumina Final report format
window
Sliding window size (in SNPs)
step
Sliding window step (in SNPs)
Details
This function can be used to inspect the raw data (LRR and MAF)
of putative CNV calls. It also calculate the mean LRR in a
sliding window with default size of 100 SNPs and default step of
50 SNPs. A bar in each plot indicate the position of the call.
\newline
For convenience consider to select the data from the entire FinalREport
outside R, e.g. using awk. As an example, awk -F"\t" '{if ($1 == "sampleID" && $3 == 1)
print $0}' FinalReport.txt > chr1_sampleID.tsv will select the SNPs
in chromosome 1 of a desired sample and save it as a separate file
that can be more easily loaded in R.
\newline
In any case final.rep must be a data-frame containing the data
of one single sample and the following columns: "Chr", "Position",
"Log.R.Ratio", "B.allele.Freq". Order is not relevant.
Value
pl
Author(s)
Simone Montalbano simone.montalbano@protonmail.com
SinomeM/cnv_geaRs documentation built on Dec. 4, 2020, 3:06 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Details Value Author(s)
Description
lrr_plot create scatter plots of LRR and MAF
in a selected region
Usage
1 2 | plot_lrr_maf(chr, cnv.start, cnv.end, region = 5, final.rep,
window = 100, step = 50)
|
Arguments
chr |
Chromosome where the putative CNV is present (e.g "1", not "chr1") |
cnv.start |
Start position of the CNV |
cnv.end |
End position of the CNV |
region |
Size of the region to be plotted on each side of the CNV |
final.rep |
Data frame in Illumina Final report format |
window |
Sliding window size (in SNPs) |
step |
Sliding window step (in SNPs) |
Details
This function can be used to inspect the raw data (LRR and MAF)
of putative CNV calls. It also calculate the mean LRR in a
sliding window with default size of 100 SNPs and default step of
50 SNPs. A bar in each plot indicate the position of the call.
\newline
For convenience consider to select the data from the entire FinalREport
outside R, e.g. using awk. As an example, awk -F"\t" '{if ($1 == "sampleID" && $3 == 1)
print $0}' FinalReport.txt > chr1_sampleID.tsv will select the SNPs
in chromosome 1 of a desired sample and save it as a separate file
that can be more easily loaded in R.
\newline
In any case final.rep must be a data-frame containing the data
of one single sample and the following columns: "Chr", "Position",
"Log.R.Ratio", "B.allele.Freq". Order is not relevant.
Value
pl
Author(s)
Simone Montalbano simone.montalbano@protonmail.com
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.