Version 0.1.0 is a major update to sceptre. Usability
and speed are improved considerably.
There is now a single interface to the sceptre
algorithm: the function run_sceptre_high_moi (previously
called run_sceptre_in_memory). The function
run_sceptre_gRNA_gene_pair, which was redundant, is now
deprecated.
run_sceptre_high_moi is much simpler to use.
run_sceptre_high_moi now has only four required arguments:
gene_matrix (previously called
expression_matrix), gRNA_matrix (previously
called expression_matrix), covariate_matrix,
and gene_gRNA_pairs. The formerly required arguments
storage_dir and side are now set to
tempdir() and “both” by default. Additionally, the argument
pod_sizes is removed entirely (and handled
internally).
run_sceptre_high_moi has the additional optional
arguments full_output and parallel.
full_output controls the complexity of the data frame
outputted by the method. When full_output is set to FALSE
(the default), run_sceptre_high_moi outputs a data frame
with four columns only, all of which are easy to interpret:
gene_id, gRNA_id, p_value, and
z_value. parallel controls whether the
function is parallelized (TRUE; default) or not (FALSE).
run_sceptre_high_moi now accepts a raw (i.e.,
unthresholded) gRNA matrix or a user-thresholded gRNA matrix.
The new auxiliary function combine_gRNAs combines
gRNAs that target the same chromosomal site, facilitating this common
analysis step.
Numerous checks have been added to
run_sceptre_high_moi ensure that the input is valid. For
example, run_sceptre_high_moi checks that gene IDs and gRNA
IDs in gene_gRNA_pairs are in fact present in
gene_matrix and gRNA_matrix,
respectively.