View source: R/graphic_functions.R
plotDeletionsByBinom | R Documentation |
The plotDeletionsByBinom
function generates a graphical output of the double chromosome deletions in multiple samples.
plotDeletionsByBinom( GENE.usage.df, chain = c("IGH", "IGK", "IGL", "TRB", "TRA"), genes.low.cer = c("IGHV3-43", "IGHV3-20"), genes.dup = c("IGHD4-11", "IGHD5-18"), genes_order = NULL )
GENE.usage.df |
double chromosome deletion summary table. See details. |
chain |
the IG chain: IGH,IGK,IGL. Default is IGH. |
genes.low.cer |
a vector of IGH genes known to be with low certantiny in the binomial test. Default is IGHV3-43 and IGHV3-20 |
genes.dup |
a vector of IGH genes known to have a duplicated gene. Default is IGHD4-11 that his duplicate is IGHD4-4 and IGHD5-18 that his duplicate is IGHD5-5 |
genes_order |
A vector of the genes by the desired order. Default is by GENE.loc |
A data.frame
created by binom_test_deletion
.
A double chromosome deletion visualization.
# Load example data and germlines data(samples_db) # Infering haplotype deletions_db = deletionsByBinom(samples_db); plotDeletionsByBinom(deletions_db)
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