doubletrouble aims to identify duplicated genes from whole-genome protein sequences and classify them based on their modes of duplication. The duplication modes are i. segmental duplication (SD); ii. tandem duplication (TD); iii. proximal duplication (PD); iv. transposed duplication (TRD) and; v. dispersed duplication (DD). Transposon-derived duplicates (TRD) can be further subdivided into rTRD (retrotransposon-derived duplication) and dTRD (DNA transposon-derived duplication). If users want a s
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library(doubletrouble)
library(syntenet)
# Load example data
data(yeast_seq)
data(yeast_annot)
data(diamond_intra)
# Prepare input data
pdata <- process_input(yeast_seq, yeast_annot)
# Classify gene pairs using the standard scheme
c_standard <- classify_gene_pairs(
annotation = pdata$annotation,
blast_list = diamond_intra,
scheme = "standard"
)
# Calculate duplicate frequencies
table(c_standard$Scerevisiae$type)
Note: Inputs are processed protein sequences and gene annotations along with intraspecies DIAMOND search results; output is a list of classified duplicated gene pairs.
classify_gene_pairs.syntenet functions like process_input and run_diamond instead.AAStringSet objects containing translated sequences of the primary transcripts.GRanges objects containing genomic coordinates of all features.run_diamond).GRangesList object).setequal(names(seqs), names(annotation)).collapse_bidirectional_hits before classification.syntenet for synteny detection and running DIAMOND alignments.还没有评价。欢迎分享你的使用感受。
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