Handler function for GET requests from Figshare
get_figshare(
file_name = NA,
item = "19700056",
output_dir = tempdir(),
return_list = FALSE
)Downloads necessary annotation files from Figshare and reads them in as data frames.
# \donttest{
get_figshare(
return_list = TRUE,
output_dir = tempdir()
)
#>
Downloading: 3.4 kB
Downloading: 3.4 kB
Downloading: 3.4 kB
Downloading: 3.4 kB
#> id name size
#> 1 34989865 Achilles_cell_line_efficacy.csv 28656
#> 2 35020903 sample_info.csv 461812
#> 3 34989868 Achilles_cell_line_growth_rate.csv 28566
#> 4 34989871 Achilles_common_essentials.csv 25883
#> 5 34989874 Achilles_dropped_guides.csv 188556
#> 6 34989877 Achilles_guide_efficacy.csv 2832269
#> 7 34989880 Achilles_guide_map.csv 4012794
#> 8 34989883 Achilles_high_variance_genes.csv 7227
#> 9 34989886 Achilles_gene_dependency.csv 345057026
#> 10 34989889 Achilles_gene_effect.csv 352646659
#> 11 34989892 Achilles_gene_effect_uncorrected.csv 358061824
#> 12 34989895 Achilles_logfold_change_failures.csv 251017335
#> 13 34989901 Achilles_metadata.csv 65036
#> 14 34989904 Achilles_raw_readcounts.csv 890882590
#> 15 34989910 Achilles_raw_readcounts_failures.csv 76580967
#> 16 34989913 Achilles_replicate_map.csv 103773
#> 17 34989916 Achilles_replicate_QC_report_failing.csv 290973
#> 18 34989919 CCLE_expression.csv 428612351
#> 19 34989922 CCLE_expression_full.csv 857722211
#> 20 34989928 CCLE_expression_proteincoding_genes_expected_count.csv 159831957
#> 21 34989931 CCLE_fusions.csv 10147141
#> 22 34989934 CCLE_fusions_unfiltered.csv 85101250
#> 23 34989937 CCLE_gene_cn.csv 840532069
#> 24 34989940 CCLE_mutations.csv 258051137
#> 25 34989943 CCLE_mutations_bool_damaging.csv 61683448
#> 26 34989946 CCLE_mutations_bool_hotspot.csv 28623366
#> 27 34989949 CCLE_mutations_bool_nonconserving.csv 66448750
#> 28 34989952 CCLE_mutations_bool_otherconserving.csv 137389
#> 29 34989955 Achilles_logfold_change.csv 2904244602
#> 30 34989958 CCLE_RNAseq_reads.csv 372776568
#> 31 34989970 CCLE_segment_cn.csv 36741691
#> 32 34989985 CCLE_expression_transcripts_expected_count.csv 1559945467
#> 33 34990018 CCLE_wes_gene_cn.csv 1819922377
#> 34 34990021 CCLE_wes_segment_cn.csv 16841624
#> 35 34990024 common_essentials.csv 17020
#> 36 34990027 CRISPR_common_essentials.csv 26240
#> 37 34990030 CRISPR_dataset_sources.csv 20595
#> 38 34990033 CRISPR_gene_dependency.csv 376767460
#> 39 34990036 CRISPR_gene_effect.csv 387091918
#> 40 34990048 CCLE_RNAseq_transcripts.csv 3513461590
#> 41 34990051 nonessentials.csv 11492
#> 42 34990054 README.txt 21109
#> is_link_only download_url
#> 1 FALSE https://ndownloader.figshare.com/files/34989865
#> 2 FALSE https://ndownloader.figshare.com/files/35020903
#> 3 FALSE https://ndownloader.figshare.com/files/34989868
#> 4 FALSE https://ndownloader.figshare.com/files/34989871
#> 5 FALSE https://ndownloader.figshare.com/files/34989874
#> 6 FALSE https://ndownloader.figshare.com/files/34989877
#> 7 FALSE https://ndownloader.figshare.com/files/34989880
#> 8 FALSE https://ndownloader.figshare.com/files/34989883
#> 9 FALSE https://ndownloader.figshare.com/files/34989886
#> 10 FALSE https://ndownloader.figshare.com/files/34989889
#> 11 FALSE https://ndownloader.figshare.com/files/34989892
#> 12 FALSE https://ndownloader.figshare.com/files/34989895
#> 13 FALSE https://ndownloader.figshare.com/files/34989901
#> 14 FALSE https://ndownloader.figshare.com/files/34989904
#> 15 FALSE https://ndownloader.figshare.com/files/34989910
#> 16 FALSE https://ndownloader.figshare.com/files/34989913
#> 17 FALSE https://ndownloader.figshare.com/files/34989916
#> 18 FALSE https://ndownloader.figshare.com/files/34989919
#> 19 FALSE https://ndownloader.figshare.com/files/34989922
#> 20 FALSE https://ndownloader.figshare.com/files/34989928
#> 21 FALSE https://ndownloader.figshare.com/files/34989931
#> 22 FALSE https://ndownloader.figshare.com/files/34989934
#> 23 FALSE https://ndownloader.figshare.com/files/34989937
#> 24 FALSE https://ndownloader.figshare.com/files/34989940
#> 25 FALSE https://ndownloader.figshare.com/files/34989943
#> 26 FALSE https://ndownloader.figshare.com/files/34989946
#> 27 FALSE https://ndownloader.figshare.com/files/34989949
#> 28 FALSE https://ndownloader.figshare.com/files/34989952
#> 29 FALSE https://ndownloader.figshare.com/files/34989955
#> 30 FALSE https://ndownloader.figshare.com/files/34989958
#> 31 FALSE https://ndownloader.figshare.com/files/34989970
#> 32 FALSE https://ndownloader.figshare.com/files/34989985
#> 33 FALSE https://ndownloader.figshare.com/files/34990018
#> 34 FALSE https://ndownloader.figshare.com/files/34990021
#> 35 FALSE https://ndownloader.figshare.com/files/34990024
#> 36 FALSE https://ndownloader.figshare.com/files/34990027
#> 37 FALSE https://ndownloader.figshare.com/files/34990030
#> 38 FALSE https://ndownloader.figshare.com/files/34990033
#> 39 FALSE https://ndownloader.figshare.com/files/34990036
#> 40 FALSE https://ndownloader.figshare.com/files/34990048
#> 41 FALSE https://ndownloader.figshare.com/files/34990051
#> 42 FALSE https://ndownloader.figshare.com/files/34990054
#> supplied_md5 computed_md5 mimetype
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get_figshare(
file_name = "Achilles_common_essentials.csv",
output_dir = tempdir()
)
#>
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#> Downloading: Achilles_common_essentials.csv
#>
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#> [1] "/var/folders/2d/d8927cd105550jjcy7qy99_w0000gn/T//RtmpboDQTA/Achilles_common_essentials.csv"
# }