interactionSubsetFASTA: FASTA sequences of interactors of a specific protein
In vitkl/SLIMFinderR: Short Linear Motif Search Using QSLIMFinder, Protein Interaction Network and Binding Domain Inference
Description
Usage
Arguments
Value
Author(s)
See Also
Examples
Description
FASTA sequences of interactors of a specific protein
Usage
1
interactionSubsetFASTA(int_subset, fasta)
Arguments
int_subset
interaction_subset_from_2_sets object renamed using interactionSubsetMapID
fasta
AAStringSet renamed by recodeFASTA
Value
object of class interactionSubsetFASTA containing: FASTA sequences for interacting proteins, original interaction_subset_from_2_sets
Author(s)
Vitalii Kleshchevnikov
See Also
subset2setsBy1ID, recodeFASTA, interactionSubsetMapID
Examples
1
2
3
4
5
6
7
subset = subset2setsBy1ID(interaction_set1 = all_human_interaction,
interaction_set2 = all_viral_interaction,
seed_id = proteins_w_signif_domains[2])
# subset FASTA
subset_fasta = interactionSubsetFASTA(int_subset = subset, fasta = all.fasta$fasta)
# rename FASTA sequences to original names
subset_fasta = recodeFASTA(subset_fasta, all.fasta$names_mapping, i = 1)
vitkl/SLIMFinderR documentation built on May 3, 2019, 8:08 p.m.
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Description Usage Arguments Value Author(s) See Also Examples
Description
FASTA sequences of interactors of a specific protein
Usage
1 | interactionSubsetFASTA(int_subset, fasta)
|
Arguments
int_subset |
interaction_subset_from_2_sets object renamed using interactionSubsetMapID |
fasta |
AAStringSet renamed by recodeFASTA |
Value
object of class interactionSubsetFASTA containing: FASTA sequences for interacting proteins, original interaction_subset_from_2_sets
Author(s)
Vitalii Kleshchevnikov
See Also
subset2setsBy1ID, recodeFASTA, interactionSubsetMapID
Examples
1 2 3 4 5 6 7 | subset = subset2setsBy1ID(interaction_set1 = all_human_interaction,
interaction_set2 = all_viral_interaction,
seed_id = proteins_w_signif_domains[2])
# subset FASTA
subset_fasta = interactionSubsetFASTA(int_subset = subset, fasta = all.fasta$fasta)
# rename FASTA sequences to original names
subset_fasta = recodeFASTA(subset_fasta, all.fasta$names_mapping, i = 1)
|
R Package Documentation
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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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