View source: R/map.generator.lnc.R
map_generator_lnc | R Documentation |
Inference of orthologous lncRNAs between multiple species is performed via pairwise BLAST (reciprocal) best hit comparisons. The corresponding orthologous tables are then stored in an output folder.
map_generator_lnc(
query_file,
subjects_folder,
output_folder,
task = "blastn",
eval = "1E-5",
ortho_detection = "RBH",
max.target.seqs = 10000,
min_qry_coverage_hsp = 30,
min_qry_perc_identity = 30,
logical_connective = "AND",
min_alig_length = NULL,
comp_cores = 1,
progress_bar = TRUE,
sep = ";",
path = NULL,
...
)
query_file |
a character string specifying the path to the lncRNAs file of the query organism in |
subjects_folder |
a character string specifying the path to the folder where lncRNAs files in |
output_folder |
a character string specifying the path to the folder where output orthologous tables should be stored. |
task |
nucleotide search task option. Options are:
|
eval |
a character string specifying the e-value for BLAST based orthology inference. Please use the scientific notation. |
ortho_detection |
a character string specifying the Orthology Inference method that shall be used to perform dNdS computations. Possible options are:
|
max.target.seqs |
a numeric value specifying the number of aligned sequences to keep.
Please be aware that |
min_qry_coverage_hsp |
minimum |
min_qry_perc_identity |
minimum |
logical_connective |
character representing logical connective (either "AND" or "OR") if |
min_alig_length |
minimum |
comp_cores |
number of computing cores that shall be used to perform parallelized computations. |
progress_bar |
should a progress bar be shown. Default is |
sep |
a file separator that is used to store maps as csv file. |
path |
a character string specifying the path to the corresponding orthology inference tool. For "BH" and "RBH": path to BLAST, "PO": path to ProteinOrtho 5.07, "OrthoMCL": path to OrthoMCL. |
... |
additional parameters that shall be passed to |
Given a query organism and a set of subject organsisms that are stored in the same folder, this function crawls through all subject organsism and infers the lncRNA homologs in pairwise species comparisons.
According to Sarropoulos, I., et al. (2019) orthology detection of lncRNAs was performed by reciprocal BLAST searches. Significant hits with an e-value <= 10-3 were selected having an alignment identity >= 10% OR a minimum alignment length >= 50 nucleotides.
Hajk-Georg Drost
Sarropoulos2019orthologr
## Not run:
# example using classic blastn searches
map_generator_lnc(
query_file = system.file('seqs/ortho_thal_cds.fasta', package = 'orthologr'),
subjects_folder = system.file('seqs/map_gen_example', package = 'orthologr'),
output_folder = "orthologs_lncrna",
comp_cores = 1
)
# example using discontiguous megablast used to find somewhat distant sequences
map_generator_lnc(
query_file = system.file('seqs/ortho_thal_cds.fasta', package = 'orthologr'),
subjects_folder = system.file('seqs/map_gen_example', package = 'orthologr'),
output_folder = "orthologs_lncrna",
task = "dc-megablast",
comp_cores = 1
)
## End(Not run)
## Not run:
# parameter settings based on Sarropoulos, I., et al. (2019)
map_generator_lnc(
query_file,,
subjects_folder,
eval = 1E-3,
ortho_detection = "RBH",
output_folder,
min_qry_coverage_hsp = 0,
min_qry_perc_identity = 10,
logical_connective = "OR",
min_alig_length = 50)
## End(Not run)
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