Perform Motif and amino acid bias classification of hydroxyproline rich glycoproteins according to Johnson et al. (2017)
maab(data, ...) # S3 method for character maab(data, ...) # S3 method for data.frame maab(data, sequence, id, ...) # S3 method for list maab(data, ...) # S3 method for default maab( data = NULL, sequence, id, order = c("ext", "tyr", "prp", "agp"), gpi = NULL, get_gpi = c("bigpi", "predgpi", "netgpi", "none"), spec = 0.99, progress = FALSE, ... ) # S3 method for AAStringSet maab(data, ...)
data | A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class |
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... | currently no additional arguments are accepted apart the ones documented bellow. |
sequence | A vector of strings representing protein amino acid sequences, or the appropriate column name if a data.frame is supplied to data argument. If .fasta file path, or list with elements of class "SeqFastaAA" provided to data, this should be left blank. |
id | A vector of strings representing protein identifiers, or the appropriate column name if a data.frame is supplied to data argument. If .fasta file path, or list with elements of class "SeqFastaAA" provided to data, this should be left blank. |
order | Order of motif counting, the default is as in Johnson et al. (2017). |
gpi | A Boolean vector indicating if the corresponding id contains a GPI or not. Can be the 'is.bigpi' column from the output of get_big_pi. |
get_gpi | A string indicating if |
spec | Numeric in the 0-1 range, indicating the threshold specificity of |
progress | Boolean, whether to show the progress bar, at default set to FALSE. |
A data frame with columns:
id protein identifiers as from input
ext_sp number of extensin SPn motifs, counted using SP3,5
ext_tyr number of extensin TYR motifs, sum of matches for: [FY].Y, KHY, VY[HKDE], V.Y, YY
prp number of proline rich protein motifs, sum of matches for: PPV.[KT], PPV[QK], KKPCPP
agp number of arabinogalactan motifs, sum of matches for: [AVTG]P1,3, [ASVTG]P1,2
past_percent summed percent of "P", "A", "S" and "T" amino acids
pvyk_percent summed percent of "P", "V", "Y" and "K" amino acids
psky_percent summed percent of "P", "S", "K" and "Y" amino acids
p_percent percent of "P"
coverage the coverage of sequence by the identified motifs
maab_class determined maab class
The function provides motif and amino acid bias descriptors used for classification of HRGP's by the MAAB pipeline (Johnson et al. 2017) as well as the determined HRGP classes. The motifs are counted in a specific order ext > tyr > prp > agp, and overlapping motifs are not counted. Hence the classification depends on the order of counting, this is most noticeable for tyr and prp, we recommend using both the default order and 'order = c("ext", "prp","tyr", "agp")'.
Johnson KL, Cassin AM, Lonsdale A, Bacic A, Doblin MS, Schultz CJ. (2017) Pipeline to Identify Hydroxyproline-Rich Glycoproteins. Plant Physiol 174(2): 886-903.
library(ragp) data(at_nsp) maab_class <- maab(sequence = at_nsp$sequence, id = at_nsp$Transcript.id) head(maab_class)#> id ext_sp ext_tyr prp agp past_percent pvyk_percent psky_percent #> 1 ATCG00660.1 0 1 0 0 18.80342 14.52991 17.94872 #> 2 AT2G43600.1 0 6 0 4 21.61172 23.44322 26.73993 #> 3 AT2G28410.1 0 0 0 4 37.39130 18.26087 22.60870 #> 4 AT2G22960.1 0 0 0 3 23.91304 17.93478 23.36957 #> 5 AT2G19580.1 0 1 0 2 22.96296 21.85185 18.88889 #> 6 AT2G19690.2 0 0 0 0 20.94595 20.94595 19.59459 #> p_percent coverage maab_class #> 1 0.000000 0.02564103 0 #> 2 3.663004 0.08791209 0 #> 3 7.826087 0.06956522 0 #> 4 5.434783 0.03260870 0 #> 5 4.074074 0.02592593 0 #> 6 2.702703 0.00000000 0