import api #134

myushen · 2024-03-20T05:56:18Z

Create and export get_default_cache_dir, clear_cache functions.
Create an import API designed to verify if the provided input sce object meet the requirements for the CAQ API's functionality.
Fix issue #132

This reverts commit 7d264f3.

This reverts commit 02d4511.

multimeric

Nice use of reduce!

Some general tips, which I've also mentioned in the comments are:

Avoid :: to keep the style consistent
Avoid @ and instead prefer accessor functions

R/counts.R

R/utils.R

R/import_metadata_and_counts.R

R/counts_per_million.R

Co-authored-by: Michael Milton <[email protected]>

multimeric

Looks good! Good use of accessor functions like assay().

Incidentally I think it would be better to use either assertthat or checkmate for validation and not both. checkmate seems to be more featureful so I wouldn't mind removing assertthat entirely and replacing it with checkmate.

R/counts.R

R/utils.R

myushen added 30 commits February 29, 2024 10:51

export default_cache function, add clear_cache function

9a2b287

check metadata, gene names, positive counts, file_id

94a6edc

generate cpm from original, check subdir number match

670c10f

check metadata input has minimum set of column names and types

c816770

add check age, sex, minimum sets of input columns

1b0d608

upload meta, counts to cloud

7d264f3

add documentation

47f237a

Revert "upload meta, counts to cloud"

fd38b9e

This reverts commit 7d264f3.

add function import_metadata_counts

0e4123f

fix

0e5e27c

try fix code suggested by knitr error

02d4511

Revert "try fix code suggested by knitr error"

e802374

This reverts commit 02d4511.

remove meta_output argument, add counts_path argument

1969796

add counts_per_million function

bf8aa68

fix error

56c32ea

fix memory issue in counts_per_million

593dcc7

fix documentation

815648c

add check: cells_ cannot be duplicates when join with api

e7e9047

add checkpoint, cell_ values in metadata must be unique

62525e5

optimise code and comments

1fdea73

fix tiny issue

6aa3380

assert_that

7ba0f25

read rds, assign matrix for counts data, save HDF5

c9e0d8e

accept sce RDS as input

944535d

accept count_path_df.rds as an input

1c4aa79

roxygenise

f8bda0b

fix a missing variable

8e34280

tiny fix

bdf294b

checking whether gene set of new count data and old count data match

65b8975

change function input, accept sce rds and cache dir only

77d0b68

myushen added 12 commits March 14, 2024 17:32

fix a variable

8101da2

save created file_id_db column in metadata slot to rds

2ab8a45

fix variable

97cbfa5

accept a loaded sce_obj as input

731e877

checking whether genes in a list of SCEs overlap

90fef3a

use gene intersection if genes across SCEs do not completely overlap

5a6dad3

move check_gene_overlap function to counts.R

15628a4

optimise counts_per_million.R. interact import API with get_SCE

8e2c89c

change function documentation

2792f11

fix assert_that

1209f7c

update Rd and local checks

1ddec5e

export necessary functions. create sample_sce_obj for checking purpose

883402b

stemangiola requested a review from multimeric March 20, 2024 23:47

multimeric requested changes Mar 22, 2024

View reviewed changes

myushen and others added 2 commits March 22, 2024 15:33

Apply suggestions from code review

506ee5a

Co-authored-by: Michael Milton <[email protected]>

add suggestions and optimise code from code review

b6ee0b2

multimeric approved these changes Mar 26, 2024

View reviewed changes

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stemangiola merged commit 2e9d487 into stemangiola:master Mar 26, 2024
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import api #134

import api #134

myushen commented Mar 20, 2024

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import api #134

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