Mercurial > repos > gaelcge > r_signac_galaxy

annotate signac-add_gene_annotations.R @ 0:6e0b320d8b6a draft default tip

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"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
author gaelcge
date Tue, 02 Aug 2022 19:11:27 +0000
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1 #!/usr/bin/env Rscript
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2
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3 # Load optparse we need to check inputs
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4
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5 suppressPackageStartupMessages(require(optparse))
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6
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7 # Load common functions
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8
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9 suppressPackageStartupMessages(require(workflowscriptscommon))
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10
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11 # parse options
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12
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13 option_list = list(
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14 make_option(
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15 c("--signac-object"),
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16 action = "store",
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17 default = NA,
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18 type = 'character',
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19 help = "Filtered peak BC matrix file in h5 format."
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20 ),
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21 make_option(
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22 c("--ens-db-genome"),
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23 action = "store",
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24 default = NA,
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25 type = 'character',
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26 help = "Metadata file."
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27 ),
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28 make_option(
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29 c("--annotations"),
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30 action = "store",
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31 default = NA,
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32 type = 'character',
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33 help = "Genome version."
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34 ),
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35 make_option(
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36 c("--output-object-file"),
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37 action = "store",
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38 default = NA,
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39 type = 'character',
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40 help = "File name in which to store serialized R matrix object."
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41 )
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42 )
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43
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44 opt <- wsc_parse_args(option_list)
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45
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46 suppressPackageStartupMessages(require(Seurat))
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47 suppressPackageStartupMessages(require(Signac))
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48 suppressPackageStartupMessages(require(GenomeInfoDb))
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49 suppressPackageStartupMessages(require(EnsDb.Hsapiens.v75))
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50 suppressPackageStartupMessages(require(EnsDb.Mmusculus.v79))
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51
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52 set.seed(1234)
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53
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54 # extract gene annotations from EnsDb
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55 signac_object <- readRDS(file = opt$signac_object)
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56
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57 annotations <- GetGRangesFromEnsDb(ensdb = EnsDb.Hsapiens.v75)
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58 print(annotations)
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59
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60 # change to UCSC style since the data was mapped to hg19
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61 seqlevelsStyle(annotations) <- "UCSC"
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62 genome(annotations) <- opt$annotations
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63
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64 # add the gene information to the object
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65 Annotation(signac_object) <- annotations
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66
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67 print(signac_object)
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68
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69 # Output to a serialized R object
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70 saveRDS(signac_object, file = opt$output_object_file)