tests/testthat/_snaps/library_annotations.md

In cancerit/RCRISPR: R Functions for CRISPR-Related Analyses

read library annotation and strip ids

Code
  get_library_annotations(test_strip_lib_ann_obj)
Output
                       sgRNA                  SEQ                          LOCUS
  1 A1BGCACCTTCGAGCTGCTGCGCG CACCTTCGAGCTGCTGCGCG chr19:58858890-58858909_A1BG_-
      CHR    START      END GENE STRAND
  1 chr19 58858890 58858909 A1BG      -
                                                   TARGET
  1 A1BG:ENST00000263100.3:exon_7:chr19:58858700-58859024

read library annotation

Code
  test_lib_ann_obj
Output
  An object of class "LibraryAnnotations"
  Slot "filepath":
  [1] "test"

  Slot "id_column":
  [1] 1

  Slot "gene_column":
  [1] 7

  Slot "chr_column":
  [1] 4

  Slot "chr_start_column":
  [1] 5

  Slot "chr_end_column":
  [1] 6

  Slot "file_separator":
  [1] "\t"

  Slot "file_header":
  [1] TRUE

  Slot "annotations":
                        sgRNA                  SEQ                          LOCUS
  1 A1BG_CACCTTCGAGCTGCTGCGCG CACCTTCGAGCTGCTGCGCG chr19:58858890-58858909_A1BG_-
  2 A1BG_AAGAGCGCCTCGGTCCCAGC AAGAGCGCCTCGGTCCCAGC chr19:58861852-58861871_A1BG_+
  3 A1BG_TGGACTTCCAGCTACGGCGC TGGACTTCCAGCTACGGCGC chr19:58862932-58862951_A1BG_-
      CHR    START      END GENE STRAND
  1 chr19 58858890 58858909 A1BG      -
  2 chr19 58861852 58861871 A1BG      +
  3 chr19 58862932 58862951 A1BG      -
                                                   TARGET
  1 A1BG:ENST00000263100.3:exon_7:chr19:58858700-58859024
  2 A1BG:ENST00000263100.3:exon_6:chr19:58861717-58862035
  3 A1BG:ENST00000263100.3:exon_5:chr19:58862738-58863071

get unprocessed library annotations

Code
  get_library_annotations(test_lib_ann_obj, processed = F)
Output
                        sgRNA                  SEQ                          LOCUS
  1 A1BG_CACCTTCGAGCTGCTGCGCG CACCTTCGAGCTGCTGCGCG chr19:58858890-58858909_A1BG_-
  2 A1BG_AAGAGCGCCTCGGTCCCAGC AAGAGCGCCTCGGTCCCAGC chr19:58861852-58861871_A1BG_+
  3 A1BG_TGGACTTCCAGCTACGGCGC TGGACTTCCAGCTACGGCGC chr19:58862932-58862951_A1BG_-
      CHR    START      END GENE STRAND
  1 chr19 58858890 58858909 A1BG      -
  2 chr19 58861852 58861871 A1BG      +
  3 chr19 58862932 58862951 A1BG      -
                                                   TARGET
  1 A1BG:ENST00000263100.3:exon_7:chr19:58858700-58859024
  2 A1BG:ENST00000263100.3:exon_6:chr19:58861717-58862035
  3 A1BG:ENST00000263100.3:exon_5:chr19:58862738-58863071

get processed library annotations

Code
  get_library_annotations(test_lib_ann_obj, processed = T)
Output
                        sgRNA gene   chr    start      end
  1 A1BG_CACCTTCGAGCTGCTGCGCG A1BG chr19 58858890 58858909
  2 A1BG_AAGAGCGCCTCGGTCCCAGC A1BG chr19 58861852 58861871
  3 A1BG_TGGACTTCCAGCTACGGCGC A1BG chr19 58862932 58862951

get processed library annotations for crisprcleanr

Code
  get_library_annotations(test_lib_ann_obj, processed = T, crisprcleanr = T)
Output
                                                 CODE GENES  CHRM STARTpos
  A1BG_CACCTTCGAGCTGCTGCGCG A1BG_CACCTTCGAGCTGCTGCGCG  A1BG chr19 58858890
  A1BG_AAGAGCGCCTCGGTCCCAGC A1BG_AAGAGCGCCTCGGTCCCAGC  A1BG chr19 58861852
  A1BG_TGGACTTCCAGCTACGGCGC A1BG_TGGACTTCCAGCTACGGCGC  A1BG chr19 58862932
                              ENDpos
  A1BG_CACCTTCGAGCTGCTGCGCG 58858909
  A1BG_AAGAGCGCCTCGGTCCCAGC 58861871
  A1BG_TGGACTTCCAGCTACGGCGC 58862951

can remove guides from library object

Code
  remove_guides_from_library_annotations_object(library_annotations_object = test_lib_ann_obj,
    guides_to_remove = c("A1BG_CACCTTCGAGCTGCTGCGCG"))
Output
  An object of class "LibraryAnnotations"
  Slot "filepath":
  [1] "test"

  Slot "id_column":
  [1] 1

  Slot "gene_column":
  [1] 7

  Slot "chr_column":
  [1] 4

  Slot "chr_start_column":
  [1] 5

  Slot "chr_end_column":
  [1] 6

  Slot "file_separator":
  [1] "\t"

  Slot "file_header":
  [1] TRUE

  Slot "annotations":
                        sgRNA                  SEQ                          LOCUS
  2 A1BG_AAGAGCGCCTCGGTCCCAGC AAGAGCGCCTCGGTCCCAGC chr19:58861852-58861871_A1BG_+
  3 A1BG_TGGACTTCCAGCTACGGCGC TGGACTTCCAGCTACGGCGC chr19:58862932-58862951_A1BG_-
      CHR    START      END GENE STRAND
  2 chr19 58861852 58861871 A1BG      +
  3 chr19 58862932 58862951 A1BG      -
                                                   TARGET
  2 A1BG:ENST00000263100.3:exon_6:chr19:58861717-58862035
  3 A1BG:ENST00000263100.3:exon_5:chr19:58862738-58863071

can remove guides as dataframe from library object

Code
  remove_guides_from_library_annotations_object(library_annotations_object = test_lib_ann_obj,
    guides_to_remove = data.frame(guide = "A1BG_CACCTTCGAGCTGCTGCGCG", extra = "test"))
Output
  An object of class "LibraryAnnotations"
  Slot "filepath":
  [1] "test"

  Slot "id_column":
  [1] 1

  Slot "gene_column":
  [1] 7

  Slot "chr_column":
  [1] 4

  Slot "chr_start_column":
  [1] 5

  Slot "chr_end_column":
  [1] 6

  Slot "file_separator":
  [1] "\t"

  Slot "file_header":
  [1] TRUE

  Slot "annotations":
                        sgRNA                  SEQ                          LOCUS
  2 A1BG_AAGAGCGCCTCGGTCCCAGC AAGAGCGCCTCGGTCCCAGC chr19:58861852-58861871_A1BG_+
  3 A1BG_TGGACTTCCAGCTACGGCGC TGGACTTCCAGCTACGGCGC chr19:58862932-58862951_A1BG_-
      CHR    START      END GENE STRAND
  2 chr19 58861852 58861871 A1BG      +
  3 chr19 58862932 58862951 A1BG      -
                                                   TARGET
  2 A1BG:ENST00000263100.3:exon_6:chr19:58861717-58862035
  3 A1BG:ENST00000263100.3:exon_5:chr19:58862738-58863071

can identify guides in library object with no coordinates

Code
  get_guides_with_no_coordinates(test_lib_ann_obj_no_coords)
Output
  [1] "sg1" "sg2" "sg3"

cancerit/RCRISPR documentation built on April 26, 2023, 10:12 p.m.