kozak_IR_ranking: Rank kozak initiation sequences
In JokingHero/ORFik: Open Reading Frames in Genomics
kozak_IR_ranking R Documentation
Rank kozak initiation sequences
Description
Defined as region (-4, -1) relative to TIS
Usage
kozak_IR_ranking(cds_k, mrna, dt.ir, faFile, group.min = 10, species = "human")
Arguments
cds_k
cds ranges (GRangesList)
mrna
mrna ranges (GRangesList)
dt.ir
data.table with a column called IR, initiation rate
faFile
FaFile, BSgenome, fasta/index file path or an
ORFik experiment. This file is usually used to find the
transcript sequences from some GRangesList.
group.min
numeric, default 10. Minimum transcripts per initation
group to be included
species
("human"), which species to use,
currently supports human (Homo sapiens), zebrafish (Danio rerio) and mouse (Mus musculus).
Both scientific or common name for these species will work.
You can also specify a pfm for your own species.
Syntax of pfm is an rectangular integer matrix,
where all columns must sum to the same value, normally 100.
See example for more information.
Rows are in order: c("A", "C", "G", "T")
Value
a ggplot grid object
JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.
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| kozak_IR_ranking | R Documentation |
Rank kozak initiation sequences
Description
Defined as region (-4, -1) relative to TIS
Usage
kozak_IR_ranking(cds_k, mrna, dt.ir, faFile, group.min = 10, species = "human")
Arguments
cds_k |
cds ranges (GRangesList) |
mrna |
mrna ranges (GRangesList) |
dt.ir |
data.table with a column called IR, initiation rate |
faFile |
|
group.min |
numeric, default 10. Minimum transcripts per initation group to be included |
species |
("human"), which species to use, currently supports human (Homo sapiens), zebrafish (Danio rerio) and mouse (Mus musculus). Both scientific or common name for these species will work. You can also specify a pfm for your own species. Syntax of pfm is an rectangular integer matrix, where all columns must sum to the same value, normally 100. See example for more information. Rows are in order: c("A", "C", "G", "T") |
Value
a ggplot grid object
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.
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