SeqFeatR: A Tool to Associate FASTA Sequences and Features
Version 0.2.4

Provides user friendly methods for the identification of sequence patterns that are statistically significantly associated with a property of the sequence. For instance, SeqFeatR allows to identify viral immune escape mutations for hosts of given HLA types. The underlying statistical method is Fisher's exact test, with appropriate corrections for multiple testing, or Bayes. Patterns may be point mutations or n-tuple of mutations. SeqFeatR offers several ways to visualize the results of the statistical analyses.

Browse man pages Browse package API and functions Browse package files

AuthorBettina Budeus
Date of publication2016-10-17 12:41:09
MaintainerBettina Budeus <bettina.budeus@stud.uni-due.de>
LicenseGPL (>= 3)
Version0.2.4
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("SeqFeatR")

Man pages

assocpair: Finding pairs of alignment positions that jointly mutate
assocpairfeat: Finding pairs of sequence alignment positions associated with...
assocpoint: Searches for associations of single alignment positions with...
assocpointhierarchical: Searches for associations of single alignment positions with...
assocpointpair: Compare results of SeqFeatRs assocpoint with SeqFeatRs...
assoctuple: Searches for associations of a tuple of alignment positions...
comparewithancestral: Compares ancestral sequence with sequence alignment
foundereffectfinder: Tries to identify a founder effect in results from SeqFeatRs...
getfreqs: Get frequencies for amino acids/nucleotides in alignment...
orPlot: Visualize odds ratios and p-values from SeqFeatRs assocpoint
q-values: Calculate q-values from p-values
rewritetuple: Rewrite result from SeqFeatRs assoctuple
SeqFeatR_GUI: GUI for SeqFeatR
SeqFeatR-package: Associates point and tuple mutations with sequence features.
smallmanhattan: A small version of manhattan plot
tartan: Visualize association of mutation pairs and features from two...
visualizepair: Visualize pairs of alignment positions that jointly mutate
visualizepairfeat: Visualize pairs of sequence alignment positions associated...
volcanoplot: Create volcano plot

Functions

HLA_and_tree_inner Source code
KD Source code
SeqFeatR-package Man page
SeqFeatR_GUI Man page
about Source code
add_correction Source code
add_correction_cm Source code
addtolist Source code
assocpair Man page
assocpairfeat Man page
assocpoint Man page
assocpointhierarchical Man page
assocpointpair Man page
assoctuple Man page
attach.config Source code
bayes_fac Source code
both_are_different Source code
calculate_co_mut Source code
calculate_co_mut_graphics Source code
calculate_co_mut_graphics_both Source code
calculate_founder Source code
calculate_length Source code Source code Source code
calculate_pos_epi Source code
calculate_pos_epi_further Source code
calculate_q_value Source code
calculate_qvalues_inner Source code
check_K Source code
check_allels Source code
check_bayes_factor Source code
check_dna Source code
check_for_pos_epi_mut_core_inner Source code
check_ident Source code
check_offset Source code
check_phylo Source code
cm_wo_create_mini_table Source code
cm_wo_inside_main Source code
cm_wo_main Source code
cm_wo_make_HLA_types_array Source code
cm_wo_make_char_array Source code
cm_wo_make_pair_array Source code
comparewithancestral Man page
create_ancestral_sequences Source code
create_correct_FASTA_input Source code Source code Source code Source code Source code Source code Source code Source code
create_mini_table_tr Source code
create_pos_epi_csv Source code Source code
create_pos_epi_plot Source code Source code
create_sequence_graphic_G Source code
create_sequence_graphic_inner Source code
easyGregexpr Source code Source code
find.neqzero Source code Source code Source code Source code Source code
find_epitope_in_given_sequence Source code Source code
find_possible_epitopes_inner Source code
find_possible_epitopes_inner_hierach Source code
find_smallest_cluster_number Source code Source code
founder_eliminator_main_inner Source code
foundereffectfinder Man page
generate_example_config Source code
generate_example_config_wo_HLA Source code
generate_example_fasta Source code
get.threshold.f.fisher.pair Source code
getFASTAfile Source code
get_10_based Source code Source code
get_AA_from_consensus Source code
get_ancestral_for_this_position Source code
get_freqs Source code
get_freqs_inner Source code
get_identifier Source code
get_intres Source code
get_label_right Source code
get_original_sequence Source code
get_original_sequence_ph Source code
get_p_fish Source code
get_seqs_for_certain_position Source code
get_shared_mutations_inside Source code
getcsvfile Source code
getfreqs Man page
getnexusfile Source code
inside_main Source code
inside_main_tr Source code
mai Source code
main Source code
make_HLA_types_array Source code
make_array Source code
make_char_array Source code Source code
make_fisher_test Source code Source code Source code
make_pair_array Source code
make_spare_room Source code
make_special_pair_array Source code Source code
open_tutorial Source code
orPlot Man page
qvalues Man page
read.config Source code
remove.zeroes Source code Source code Source code Source code Source code Source code Source code
remove_only_ones Source code
reverselog_trans Source code
rewrite_shared_mutations Source code
rewrite_shared_mutations_result_inner Source code
rewritetuple Man page
rotate Source code
save_config Source code
shared_mutations Source code
small_manhattan Source code
smallmanhattan Man page Source code
smallmanhattan_inner Source code
tartan Man page
test_for_comutation_inner Source code
test_for_comutation_only_graphics_inner Source code
test_for_comutation_only_graphics_wo_allels_2_inner Source code
test_for_comutation_only_graphics_wo_allels_inner Source code
test_for_comutation_without_allel_inner Source code
test_for_occurence Source code Source code
test_if_in_one_cluster Source code Source code
test_if_same_branch Source code
test_if_same_subtree Source code
two_wo_set_input_file_known_sequences Source code
visualizepair Man page
visualizepairfeat Man page
volcanoplot Man page
volcanoplot_inner Source code

Files

inst
inst/CITATION
inst/extdata
inst/extdata/Example_reference_nt.fasta
inst/extdata/assocpairfeat_results.csv
inst/extdata/Example_model_for_bayes.txt
inst/extdata/Example_nt.fasta
inst/extdata/Example_epitopes_aa.csv
inst/extdata/Example_HLA_binding_motifs_nt.csv
inst/extdata/Example_aa.fasta
inst/extdata/Example_reference_aa.fasta
inst/extdata/tart_1.csv
inst/extdata/Example_tree.nh
inst/extdata/Example_Consensus_nt.fasta
inst/extdata/shared_mutations_result_for_tartan.csv
inst/extdata/Example_Consensus_aa.fasta
inst/extdata/config.cfg
inst/extdata/Example_epitopes_nt.csv
inst/extdata/Example_HLA_binding_motifs_aa.csv
inst/extdata/Example_aa_for_cwa.fasta
inst/extdata/assocpoint_results.csv
inst/extdata/assocpair_results.csv
inst/extdata/assoctuple_result.csv
inst/extdata/tart_2.csv
inst/extdata/assocpoint_results_nt.csv
inst/doc
inst/doc/SeqFeatR_tutorial.pdf
inst/doc/SeqFeatR_tutorial.Rnw
NAMESPACE
INSTALL
NEWS
R
R/orPlot.R
R/visualizepair.R
R/assocpoint.R
R/assocpointpair.R
R/assocpair.R
R/rewritetuple.R
R/assocpairfeat.R
R/SeqFeatR_GUI.R
R/foundereffectfinder.R
R/volcanoplot.R
R/visualizepairfeat.R
R/smallmanhattan.R
R/comparewithancestral.R
R/tartan.R
R/getfreqs.R
R/q-values.R
R/assoctuple.R
R/assocpointhierarchical.R
vignettes
vignettes/log.pdf_tex
vignettes/phylo_ex.svg
vignettes/Example_HLA_position.png
vignettes/screenshotHLA.png
vignettes/phylo_ex.pdf_tex
vignettes/SeqFeatR_tutorial.Rnw
vignettes/phylo_ex.pdf
vignettes/tart.pdf
vignettes/log.pdf
vignettes/OR_new.pdf
vignettes/tart.pdf_tex
vignettes/OR_new.pdf_tex
MD5
build
build/vignette.rds
DESCRIPTION
man
man/foundereffectfinder.Rd
man/q-values.Rd
man/rewritetuple.Rd
man/volcanoplot.Rd
man/assoctuple.Rd
man/orPlot.Rd
man/assocpair.Rd
man/SeqFeatR_GUI.Rd
man/tartan.Rd
man/SeqFeatR-package.Rd
man/smallmanhattan.Rd
man/comparewithancestral.Rd
man/assocpairfeat.Rd
man/getfreqs.Rd
man/assocpointpair.Rd
man/visualizepair.Rd
man/visualizepairfeat.Rd
man/assocpoint.Rd
man/assocpointhierarchical.Rd
SeqFeatR documentation built on May 20, 2017, 4:31 a.m.