tests/testthat/_snaps/raw_count_statistics.md

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

can generate count matrix stats with one column

Code
  count_matrix_stats(count_matrix = test_count_matrix)
Output
     sample total_counts total_sgrnas zero_sgrnas pct_zero_sgrnas low_sgrnas
  1 HELA_T0          752            3           1           33.33          1
    pct_low_sgrnas gini_index
  1          33.33       0.52

can generate count matrix stats with multiple columns

Code
  count_matrix_stats(count_matrix = test_count_matrix, count_column = c(3, 5))
Output
            sample total_counts total_sgrnas zero_sgrnas pct_zero_sgrnas
  1        HELA_T0          752            3           1           33.33
  2 HELA_T15B_CTRL          602            3           1           33.33
    low_sgrnas pct_low_sgrnas gini_index
  1          1          33.33       0.52
  2          1          33.33       0.54

can generate count matrix stats with total_reads

Code
  count_matrix_stats(count_matrix = test_count_matrix, count_column = c(3, 5),
  total_reads = c(HELA_T0 = 2000, HELA_T15B_CTRL = 5120))
Output
            sample total_reads prop_mapped_reads pct_mapped_reads total_counts
  1        HELA_T0        2000           0.37600            37.60          752
  2 HELA_T15B_CTRL        5120           0.11758            11.76          602
    total_sgrnas zero_sgrnas pct_zero_sgrnas low_sgrnas pct_low_sgrnas gini_index
  1            3           1           33.33          1          33.33       0.52
  2            3           1           33.33          1          33.33       0.54

can generate count matrix stats with zeros

Code
  count_matrix_stats(count_matrix = data.frame(id = c("sg1", "sg2"), gene = c(
    "g1", "g2"), S1 = rep(0, 2), S2 = rep(0, 2)), count_column = 3:4)
Output
    sample total_counts total_sgrnas zero_sgrnas pct_zero_sgrnas low_sgrnas
  1     S1            0            2           2             100          2
  2     S2            0            2           2             100          2
    pct_low_sgrnas gini_index
  1            100         -3
  2            100         -3

can generate count matrix stats with NAs

Code
  count_matrix_stats(count_matrix = data.frame(id = c("sg1", "sg2"), gene = c(
    "g1", "g2"), S1 = c(NA, 2), S2 = rep(0, 2)), count_column = 3:4)
Output
    sample total_counts total_sgrnas zero_sgrnas pct_zero_sgrnas low_sgrnas
  1     S1            2            2           1              50          2
  2     S2            0            2           2             100          2
    pct_low_sgrnas gini_index
  1            100          0
  2            100         -3

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