phmmer_HBG2_HUMAN: phmmer_HBG2_HUMAN
In currocam/toolkit4pySCA: A set of useful functions for performing an Statistical Coupling Analysis from scratch in R and using pySCA
phmmer_HBG2_HUMAN R Documentation
phmmer_HBG2_HUMAN
Description
A list containing the results of 200 entries after searching HBG2_HUMAN sequence
in phmmer against PDB and SwissProt, then preparing the results to perform
statistical coupling analyses using pySCA.
Usage
phmmer_HBG2_HUMAN
Format
An object of class list of length 3.
Details
A list containing the following items:
df: a data frame with 1029 rows and 78 columns. It contains the results
of searching with phmmer against PDB and SwissProt. It has as many entries as
domains have been identified and is intended to make use of the group_by
function, in order to access information related to the hash 'stats' and
'sequences'. To understand the meaning of the columns, see
extract_tidy_df_from_hmmer
fullfasta: An AAStringSet from the Biostrings library containing all
completed sequences found with phmmer. It is intended to be filtered for
redundancy using unique() and with df-related information (e.g. e-value)
using [] indexes.
aln: An MsaAAMultipleAlignment of non-redundant sequences whose
e-value and the best e-value of their domains was less than 0.001. The
alignment was performed using msaClustalW.
Source
currocam/toolkit4pySCA documentation built on April 7, 2022, 8:17 p.m.
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| phmmer_HBG2_HUMAN | R Documentation |
phmmer_HBG2_HUMAN
Description
A list containing the results of 200 entries after searching HBG2_HUMAN sequence in phmmer against PDB and SwissProt, then preparing the results to perform statistical coupling analyses using pySCA.
Usage
phmmer_HBG2_HUMAN
Format
An object of class list of length 3.
Details
A list containing the following items:
df: a data frame with 1029 rows and 78 columns. It contains the results of searching with phmmer against PDB and SwissProt. It has as many entries as domains have been identified and is intended to make use of the
group_byfunction, in order to access information related to the hash 'stats' and 'sequences'. To understand the meaning of the columns, seeextract_tidy_df_from_hmmerfullfasta: An AAStringSet from the Biostrings library containing all completed sequences found with phmmer. It is intended to be filtered for redundancy using unique() and with df-related information (e.g. e-value) using [] indexes.
aln: An MsaAAMultipleAlignment of non-redundant sequences whose e-value and the best e-value of their domains was less than 0.001. The alignment was performed using msaClustalW.
Source
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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