| Title: | Peptide microarray data package |
|---|---|
| Description: | Provides sample files and data for the vignettes of pepStat and Pviz as well as peptide collections for HIV and SIV. |
| Authors: | Renan Sauteraud, Raphael Gottardo |
| Maintainer: | Renan Sauteraud <[email protected]> |
| License: | Artistic-2.0 |
| Version: | 1.32.0 |
| Built: | 2026-10-10 11:06:15 UTC |
| Source: | https://github.com/bioc/pepDat |
A peptide dataset created from the multiple alignment of the reference sequence hxb2 and the seven subtypes A, B, C, D, M, CRF01, CRF02
data(pep_hxb2)data(pep_hxb2)
A GRanges object. One row per peptide.
peptides: The rownames are 15mers from the envelope of 7 subtypes of HIV-1.
seqnames: An information regarding the genomic location of the peptide.
ranges: The start and end coordinate of the peptide based on the coordinates of the reference hxb2.
aligned: The aligned column represents the peptide as it is aligned in the multiple alignment.
trimmed: The trimmed column represents the part of hxb2's sequence aligned with the peptide.
zSums: The sum of the zScale of each amino-acid of the 15mer.
clade: A list of the subtypes which contain this peptide.
The alignments used to create this collections are available in the extdata/alignments folder, as well as the raw sequences on fasta format.
http://www.hiv.lanl.gov/content/sequence/HIV/REVIEWS/HXB2.html
Peptide collection for HXB2 and JPT clades
data(pep_hxb2JPT)data(pep_hxb2JPT)
A GRanges object. One row per peptide.
Peptide collection for SIV enveloppe
data(pep_m239smE543)data(pep_m239smE543)
A GRanges object. One row per peptide.
A peptide dataset created from the multiple alignment of the reference sequence mac239 from LANL database, our mac239 and E660 subtypes.
data(pep_mac239)data(pep_mac239)
A GRanges object. One row per peptide.
peptides: The rownames are 15mers from the envelope of mac239 and E660.
seqnames: An information regarding the genomic location of the peptide.
ranges: The start and end coordinate of the peptide based on the coordinates of the reference mac239.
aligned: The aligned column represents the peptide as it is aligned in the multiple alignment.
peptideNb:Number of the corresponding mac239 peptide.
zSums: The sum of the zScale of each amino-acid of the 15mer.
clade: A list of the subtypes which contain this peptide.
The alignments used to create this collections are available in the extdata/alignments folder, as well as the raw sequences on fasta format.
http://www.hiv.lanl.gov/content/sequence/HIV/REVIEWS/SIV_NUMBERING2001/SivNumbering.html
This is the result tables of a peptide microarray analysis using
pepStat. It summarizes the antibody binding prediction for each
peptide, depending on the group. restab_aggregate has one row per
peptide. Peptides that belong to more than one clade have a single entry.
restab has one row per peptide per clade. Each clade has
been normalized separately.
A data.frame containing 1964 rows and 9 variables for
restab. 1423 rows and 9 variables for restab_aggregate.
peptide: Peptide sequences
position: The position of peptides on the reference sequence HXB2.
space: The location of the peptide. Here, gp160, the evelope of HIV.
start: The start coordinate of the peptide on the reference sequence.
end: The end coordinate of the peptide on the reference sequence.
widt: The length of the peptides.
clade: The virus subtypes that the peptide belongs to.
group1: Frequency of antibody binding events in the subjects
of group1 for that peptide.
group2: Frequency of antibody binding events in the subjects
of group2 for that peptide.
For more information, see ?pepStat::restab.