Add gene annotations to features

Source: R/preprocessing_filtering_reduction.R

Add gene annotations to features

feature_annotation_scExp(scExp, ref = "hg38", reference_annotation = NULL)

Arguments

scExp

A SingleCellExperiment object.
ref

Reference genome. Either 'hg38' or 'mm10'. ('hg38')
reference_annotation

A data.frame containing gene (or else) annotation with genomic coordinates.

Value

A SingleCellExperiment object with annotated rowData.

Examples

scExp = create_scExp(create_scDataset_raw()$mat,create_scDataset_raw()$annot)

#> ChromSCape::create_scExp - the matrix has 300 cells and 600 features.
scExp = feature_annotation_scExp(scExp)

#> ChromSCape::feature_annotation_scExp - Selecting hg38 genes from Gencode.
head(SummarizedExperiment::rowRanges(scExp))

#> GRanges object with 6 ranges and 3 metadata columns:
#>                          seqnames            ranges strand |
#>                             <Rle>         <IRanges>  <Rle> |
#>           chr1_1_5147117     chr1         1-5147117      * |
#>    chr1_5147118_10294233     chr1  5147118-10294233      * |
#>   chr1_10294234_15441350     chr1 10294234-15441350      * |
#>   chr1_15441351_20588466     chr1 15441351-20588466      * |
#>   chr1_20588467_25735583     chr1 20588467-25735583      * |
#>   chr1_25735584_30882699     chr1 25735584-30882699      * |
#>                                              ID                   Gene
#>                                     <character>            <character>
#>           chr1_1_5147117         chr1_1_5147117 MIR1302-2, FAM138A, ..
#>    chr1_5147118_10294233  chr1_5147118_10294233 RP1-58B11.1, RP11-15..
#>   chr1_10294234_15441350 chr1_10294234_15441350 PGD, APITD1-CORT, AP..
#>   chr1_15441351_20588466 chr1_15441351_20588466 CELA2A, CELA2B, CASP..
#>   chr1_20588467_25735583 chr1_20588467_25735583 CDA, PINK1, PINK1-AS..
#>   chr1_25735584_30882699 chr1_25735584_30882699 SEPN1, RP1-317E23.6,..
#>                          distanceToTSS
#>                              <integer>
#>           chr1_1_5147117             0
#>    chr1_5147118_10294233             0
#>   chr1_10294234_15441350             0
#>   chr1_15441351_20588466             0
#>   chr1_20588467_25735583             0
#>   chr1_25735584_30882699             0
#>   -------
#>   seqinfo: 23 sequences from an unspecified genome; no seqlengths

# Mouse
scExp = create_scExp(create_scDataset_raw(ref="mm10")$mat,
  create_scDataset_raw(ref="mm10")$annot)

#> ChromSCape::create_scExp - the matrix has 300 cells and 600 features.
scExp = feature_annotation_scExp(scExp,ref="mm10")

#> ChromSCape::feature_annotation_scExp - Selecting mm10 genes from Gencode.
head(SummarizedExperiment::rowRanges(scExp))

#> GRanges object with 6 ranges and 3 metadata columns:
#>                          seqnames            ranges strand |
#>                             <Rle>         <IRanges>  <Rle> |
#>           chr1_1_4542536     chr1         1-4542536      * |
#>     chr1_4542537_9085072     chr1   4542537-9085072      * |
#>    chr1_9085073_13627607     chr1  9085073-13627607      * |
#>   chr1_13627608_18170143     chr1 13627608-18170143      * |
#>   chr1_18170144_22712679     chr1 18170144-22712679      * |
#>   chr1_22712680_27255214     chr1 22712680-27255214      * |
#>                                              ID                   Gene
#>                                     <character>            <character>
#>           chr1_1_4542536         chr1_1_4542536 Gm1992, Xkr4, Gm3738..
#>     chr1_4542537_9085072   chr1_4542537_9085072 Gm37323, Mrpl15, Lyp..
#>    chr1_9085073_13627607  chr1_9085073_13627607 Sntg1, Rrs1, Adhfe1,..
#>   chr1_13627608_18170143 chr1_13627608_18170143 Lactb2, Xkr9, Eya1, ..
#>   chr1_18170144_22712679 chr1_18170144_22712679 Defb18, Defb41, Gm29..
#>   chr1_22712680_27255214 chr1_22712680_27255214 Rims1, 4933415F23Rik..
#>                          distanceToTSS
#>                              <integer>
#>           chr1_1_4542536             0
#>     chr1_4542537_9085072             0
#>    chr1_9085073_13627607             0
#>   chr1_13627608_18170143             0
#>   chr1_18170144_22712679             0
#>   chr1_22712680_27255214             0
#>   -------
#>   seqinfo: 21 sequences from an unspecified genome; no seqlengths