tests/testthat/_snaps/sample_counts.md

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

get original counts

Code
  counts(test_unordered_counts)
Output
                        sgRNA GENE HELA_T0
  1 A1BG_CACCTTCGAGCTGCTGCGCG A1BG     478
  2 1000_AAGAGCGCCTCGGTCCCAGC 1000       0
  3 0001_AAGAGCGCCTCGGTCCCAGC 0001       3
  4 A1BG_TGGACTTCCAGCTACGGCGC A1BG     274
  5 AABC_TGGACTTCCAGCTACGGCGC AABC      12

get unsorted processed counts

Code
  counts(test_unordered_counts, processed = T)
Output
                        sgRNA gene HELA_T0
  1 A1BG_CACCTTCGAGCTGCTGCGCG A1BG     478
  2 1000_AAGAGCGCCTCGGTCCCAGC 1000       0
  3 0001_AAGAGCGCCTCGGTCCCAGC 0001       3
  4 A1BG_TGGACTTCCAGCTACGGCGC A1BG     274
  5 AABC_TGGACTTCCAGCTACGGCGC AABC      12

get sorted processed counts

Code
  counts(test_unordered_counts, processed = T, sort_ids = T)
Output
                        sgRNA gene HELA_T0
  3 0001_AAGAGCGCCTCGGTCCCAGC 0001       3
  2 1000_AAGAGCGCCTCGGTCCCAGC 1000       0
  1 A1BG_CACCTTCGAGCTGCTGCGCG A1BG     478
  4 A1BG_TGGACTTCCAGCTACGGCGC A1BG     274
  5 AABC_TGGACTTCCAGCTACGGCGC AABC      12

read uncompressed sample count file

Code
  test_counts
Output
  An object of class "SampleCounts"
  Slot "sample_name":
  [1] "HELA_T0"

  Slot "filepath":
  [1] "test"

  Slot "id_column":
  [1] 1

  Slot "gene_column":
  [1] 2

  Slot "count_column":
  [1] 3

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

  Slot "file_header":
  [1] TRUE

  Slot "counts":
                        sgRNA GENE HELA_T0
  1 A1BG_CACCTTCGAGCTGCTGCGCG A1BG     478
  2 A1BG_AAGAGCGCCTCGGTCCCAGC A1BG       0
  3 A1BG_TGGACTTCCAGCTACGGCGC A1BG     274

read gzipped sample count file

Code
  gzipped_test_counts
Output
  An object of class "SampleCounts"
  Slot "sample_name":
  [1] "CTRL_HELA_T15A"

  Slot "filepath":
  [1] "test.gz"

  Slot "id_column":
  [1] 1

  Slot "gene_column":
  [1] 2

  Slot "count_column":
  [1] 3

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

  Slot "file_header":
  [1] TRUE

  Slot "counts":
                        sgRNA GENE HELA_T15A_CTRL
  1 A1BG_CACCTTCGAGCTGCTGCGCG A1BG            519
  2 A1BG_AAGAGCGCCTCGGTCCCAGC A1BG              0
  3 A1BG_TGGACTTCCAGCTACGGCGC A1BG            193

read sample count file and strip ids

Code
  test_counts_stripped
Output
  An object of class "SampleCounts"
  Slot "sample_name":
  [1] "HELA_T0"

  Slot "filepath":
  [1] "test"

  Slot "id_column":
  [1] 1

  Slot "gene_column":
  [1] 2

  Slot "count_column":
  [1] 3

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

  Slot "file_header":
  [1] TRUE

  Slot "counts":
      id gene s1
  1 xy12   g1  1

read sample count file with numeric sample names

Code
  test_counts_numeric_sample
Output
  An object of class "SampleCounts"
  Slot "sample_name":
  [1] "1HELA_T0"

  Slot "filepath":
  [1] "test"

  Slot "id_column":
  [1] 1

  Slot "gene_column":
  [1] 2

  Slot "count_column":
  [1] 3

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

  Slot "file_header":
  [1] TRUE

  Slot "counts":
                        sgRNA GENE 1HELA_T0
  1 A1BG_CACCTTCGAGCTGCTGCGCG A1BG      478
  2 A1BG_AAGAGCGCCTCGGTCCCAGC A1BG        0
  3 A1BG_TGGACTTCCAGCTACGGCGC A1BG      274

combine SampleCounts objects into count matrix

Code
  test_count_matrix
Output
                        sgRNA gene HELA_T0 CTRL_HELA_T15A
  1 A1BG_AAGAGCGCCTCGGTCCCAGC A1BG       0              0
  2 A1BG_CACCTTCGAGCTGCTGCGCG A1BG     478            519
  3 A1BG_TGGACTTCCAGCTACGGCGC A1BG     274            193

combine SampleCounts objects into count matrix and sort ids

Code
  test_count_matrix
Output
                        sgRNA gene HELA_T0 CTRL_HELA_T15A
  1 A1BG_AAGAGCGCCTCGGTCCCAGC A1BG       0              0
  2 A1BG_CACCTTCGAGCTGCTGCGCG A1BG     478            519
  3 A1BG_TGGACTTCCAGCTACGGCGC A1BG     274            193

can read count matrix file

Code
  read_count_matrix_file(test_count_matrix_file, id_column = 1, gene_column = 2,
    count_column = "3")
Output
                        sgRNA GENE HELA_T0
  1 A1BG_CACCTTCGAGCTGCTGCGCG A1BG     478
  2 A1BG_AAGAGCGCCTCGGTCCCAGC A1BG       0
  3 A1BG_TGGACTTCCAGCTACGGCGC A1BG     274

can read count matrix file returning processed matrix

Code
  read_count_matrix_file(test_count_matrix_file, id_column = 1, gene_column = 2,
    count_column = "3", processed = T)
Output
                        sgRNA gene HELA_T0
  1 A1BG_CACCTTCGAGCTGCTGCGCG A1BG     478
  2 A1BG_AAGAGCGCCTCGGTCCCAGC A1BG       0
  3 A1BG_TGGACTTCCAGCTACGGCGC A1BG     274

can read count matrix file and strip ids

Code
  read_count_matrix_file(filepath = system.file("testdata",
    "test_counts_strip_ids.tsv", package = "rcrispr"), id_column = 1,
  gene_column = 2, count_column = "3", processed = T, strip_ids = T)
Output
    sgRNA gene s1
  1  xy12   g1  1

can read count matrix file and sort ids

Code
  read_count_matrix_file(filepath = test_count_matrix_file, id_column = 1,
    gene_column = 2, count_column = "3", processed = T, sort_ids = T)
Output
                        sgRNA gene HELA_T0
  2 A1BG_AAGAGCGCCTCGGTCCCAGC A1BG       0
  1 A1BG_CACCTTCGAGCTGCTGCGCG A1BG     478
  3 A1BG_TGGACTTCCAGCTACGGCGC A1BG     274

can read sample count files

Code
  count_objects
Output
  [[1]]
  An object of class "SampleCounts"
  Slot "sample_name":
  [1] "HELA_T0"

  Slot "filepath":
  [1] "test"

  Slot "id_column":
  [1] 1

  Slot "gene_column":
  [1] 2

  Slot "count_column":
  [1] 3

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

  Slot "file_header":
  [1] TRUE

  Slot "counts":
                        sgRNA GENE HELA_T0
  1 A1BG_CACCTTCGAGCTGCTGCGCG A1BG     478
  2 A1BG_AAGAGCGCCTCGGTCCCAGC A1BG       0
  3 A1BG_TGGACTTCCAGCTACGGCGC A1BG     274


  [[2]]
  An object of class "SampleCounts"
  Slot "sample_name":
  [1] "CTRL_HELA_T15A"

  Slot "filepath":
  [1] "test"

  Slot "id_column":
  [1] 1

  Slot "gene_column":
  [1] 2

  Slot "count_column":
  [1] 3

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

  Slot "file_header":
  [1] TRUE

  Slot "counts":
                        sgRNA GENE HELA_T15A_CTRL
  1 A1BG_CACCTTCGAGCTGCTGCGCG A1BG            519
  2 A1BG_AAGAGCGCCTCGGTCCCAGC A1BG              0
  3 A1BG_TGGACTTCCAGCTACGGCGC A1BG            193

can reorder count matrix

Code
  reorder_count_matrix_by_sample_type(count_matrix = sample_count_matrix,
    sample_metadata_object = test_metadata_obj)
Output
                        sgRNA gene HELA_T0 CTRL_HELA_T15A
  1 A1BG_AAGAGCGCCTCGGTCCCAGC A1BG       0              0
  2 A1BG_CACCTTCGAGCTGCTGCGCG A1BG     478            519
  3 A1BG_TGGACTTCCAGCTACGGCGC A1BG     274            193

can remove guides from sample counts

Code
  remove_guides_from_sample_counts(sample_counts_object = test_counts,
    guides_to_remove = c("A1BG_CACCTTCGAGCTGCTGCGCG"))
Output
  An object of class "SampleCounts"
  Slot "sample_name":
  [1] "HELA_T0"

  Slot "filepath":
  [1] "test"

  Slot "id_column":
  [1] 1

  Slot "gene_column":
  [1] 2

  Slot "count_column":
  [1] 3

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

  Slot "file_header":
  [1] TRUE

  Slot "counts":
                        sgRNA GENE HELA_T0
  2 A1BG_AAGAGCGCCTCGGTCCCAGC A1BG       0
  3 A1BG_TGGACTTCCAGCTACGGCGC A1BG     274

can remove guides as dataframe from sample counts

Code
  remove_guides_from_sample_counts(sample_counts_object = test_counts,
    guides_to_remove = data.frame(guide = "A1BG_CACCTTCGAGCTGCTGCGCG", extra = "test"))
Output
  An object of class "SampleCounts"
  Slot "sample_name":
  [1] "HELA_T0"

  Slot "filepath":
  [1] "test"

  Slot "id_column":
  [1] 1

  Slot "gene_column":
  [1] 2

  Slot "count_column":
  [1] 3

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

  Slot "file_header":
  [1] TRUE

  Slot "counts":
                        sgRNA GENE HELA_T0
  2 A1BG_AAGAGCGCCTCGGTCCCAGC A1BG       0
  3 A1BG_TGGACTTCCAGCTACGGCGC A1BG     274

can remove guides from count matrix

Code
  remove_guides_from_count_matrix(count_matrix = test_count_matrix, id_column = 1,
    guides_to_remove = c("A1BG_CACCTTCGAGCTGCTGCGCG"))
Output
                        sgRNA gene HELA_T0 HELA_T15A_CTRL HELA_T15B_CTRL
  2 A1BG_AAGAGCGCCTCGGTCCCAGC A1BG       0              0              0
  3 A1BG_TGGACTTCCAGCTACGGCGC A1BG     274            193            163
    HELA_T15C_CTRL HELA_T15A_OLA HELA_T15B_OLA HELA_T15C_OLA
  2             52             0            16             0
  3            161            80           393            45

can remove guides as dataframe from count matrix

Code
  remove_guides_from_count_matrix(count_matrix = test_count_matrix, id_column = 1,
    guides_to_remove = data.frame(guide = "A1BG_CACCTTCGAGCTGCTGCGCG", extra = "test"))
Output
                        sgRNA gene HELA_T0 HELA_T15A_CTRL HELA_T15B_CTRL
  2 A1BG_AAGAGCGCCTCGGTCCCAGC A1BG       0              0              0
  3 A1BG_TGGACTTCCAGCTACGGCGC A1BG     274            193            163
    HELA_T15C_CTRL HELA_T15A_OLA HELA_T15B_OLA HELA_T15C_OLA
  2             52             0            16             0
  3            161            80           393            45

can compare sample metadata to count matrix

Code
  compare_matrix_to_sample_metadata(data = test_count_matrix,
    sample_metadata_object = test_metadata_obj)
Output
  [1] TRUE

can get guides failing filter

Code
  get_guides_failing_filter(count_matrix = test_count_matrix, count_column = 3:4,
  filter_indices = 3:4)
Output
  [1] "A1BG_AAGAGCGCCTCGGTCCCAGC"

get guides failing filter with filter_method any

Code
  get_guides_failing_filter(count_matrix = test_count_matrix, count_column = 3:4,
  filter_indices = 3:4, min_reads = 200, filter_method = "any")
Output
  [1] "A1BG_AAGAGCGCCTCGGTCCCAGC" "A1BG_TGGACTTCCAGCTACGGCGC"

get guides failing filter with filter_method all

Code
  get_guides_failing_filter(count_matrix = test_count_matrix, count_column = 3:4,
  filter_indices = 3:4, min_reads = 200, filter_method = "all")
Output
  [1] "A1BG_AAGAGCGCCTCGGTCCCAGC"

get guides failing filter with filter_method mean

Code
  get_guides_failing_filter(count_matrix = test_count_matrix, count_column = 3:4,
  filter_indices = 3:4, min_reads = 200, filter_method = "mean")
Output
  [1] "A1BG_AAGAGCGCCTCGGTCCCAGC"

get guides failing filter with filter_method median

Code
  get_guides_failing_filter(count_matrix = test_count_matrix, count_column = 3:4,
  filter_indices = 3:4, min_reads = 200, filter_method = "median")
Output
  [1] "A1BG_AAGAGCGCCTCGGTCCCAGC"

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