ptm (version 0.2.2)

parse.hssp: Parse a HSSP File to Return Dataframes

Description

Parses a HSSP file to return dataframes.

Usage

parse.hssp(file, keepfiles = FALSE)

Arguments

file

input hssp file.

keepfiles

logical, if TRUE the dataframes will be saved in the working directory and we will keep the hssp file.

Value

Returns a dataframe corresponding to the profile.Rda described above.

Details

If the argument 'keepfiles' is not set to TRUE, the hssp file used to get the parsed dataframe will be removed. Otherwise, 4 dataframes will be saved:

• id_seq_list.Rda: This block of information holds the metadata per sequence, and some alignment statistic. See https://swift.cmbi.umcn.nl/gv/hssp for a detailed description of the information that can be find in this block.

• id_aln.Rda: This dataframe contains the alignment itself (each sequence is a column). Additional information such as secondary structure, SASA, etc., is also found in this block.

• id_profile.Rda: This dataframe holds per amino acid type its percentage in the list of residues observed at that position. In addition, this dataframe also informs about the entropy at each position, as well as the number of sequences spanning this position (NOOC).

• id_insertions.Rda: A dataframe with information regarding those sequences that contain insertions. See https://swift.cmbi.umcn.nl/gv/hssp for further details.

References

Touw et al (2015) Nucl. Ac. Res. 43:D364-368.

See Also

msa(), custom.aln(), list.hom(), get.hssp(), shannon()

Examples

# NOT RUN {
parse.hssp(file = './1u8f.hssp')
# }