R/allEndpoints.R
get_dataset_processed_expression.RdRetrieve processed expression data of a dataset
A numerical dataset identifier or a dataset short name
TRUE to receive results as-is from Gemma, or FALSE to enable
parsing. Raw results usually contain additional fields and flags that are
omitted in the parsed results.
Whether or not to save to cache for future calls with the
same inputs and use the result saved in cache if a result is already saved.
Doing options(gemma.memoised = TRUE) will ensure that the cache is always
used. Use forget_gemma_memoised to clear the cache.
The name of a file to save the results to, or NULL to not write
results to a file. If raw == TRUE, the output will be the raw endpoint from the
API, likely a JSON or a gzip file. Otherwise, it will be a RDS file.
Whether or not to overwrite if a file exists at the specified filename.
If raw is FALSE (default), a data table of the expression matrix for the queried dataset. If raw is TRUE, returns the binary file in raw form.
get_dataset_processed_expression("GSE2018")
#> Probe GeneSymbol
#> <char> <char>
#> 1: 1007_s_at DDR1
#> 2: 1053_at RFC2
#> 3: 117_at HSPA7|HSPA6
#> 4: 121_at PAX8
#> 5: 1255_g_at GUCA1ANB-GUCA1A|GUCA1A
#> ---
#> 22279: AFFX-r2-Hs28SrRNA-3_at
#> 22280: AFFX-r2-Hs28SrRNA-5_at
#> 22281: AFFX-r2-Hs28SrRNA-M_at
#> 22282: AFFX-r2-P1-cre-3_at
#> 22283: AFFX-r2-P1-cre-5_at
#> GeneName
#> <char>
#> 1: discoidin domain receptor tyrosine kinase 1
#> 2: replication factor C subunit 2
#> 3: heat shock protein family A (Hsp70) member 7 (pseudogene)|heat shock protein family A (Hsp70) member 6
#> 4: paired box 8
#> 5: GUCA1ANB-GUCA1A readthrough|guanylate cyclase activator 1A
#> ---
#> 22279:
#> 22280:
#> 22281:
#> 22282:
#> 22283:
#> NCBIid BAL_1_A0B0 BAL_27a_A0B0 BAL_43_A0B0 BAL_13_A0B0
#> <char> <num> <num> <num> <num>
#> 1: 780 7.4623 7.8763 7.4546 7.5897
#> 2: 5982 7.0674 6.8416 6.9020 6.8889
#> 3: 3311|3310 7.8392 7.7334 7.6140 7.7068
#> 4: 7849 9.1243 9.3388 9.1342 9.0008
#> 5: 118142757|2978 4.1629 4.0015 3.9937 4.0622
#> ---
#> 22279: 6.0442 5.8953 6.0414 5.7437
#> 22280: 4.3702 4.4491 4.3248 4.2274
#> 22281: 5.8420 5.5735 5.6337 5.4054
#> 22282: 12.4001 12.3097 12.7080 12.6076
#> 22283: 12.4956 12.3234 12.7085 12.6159
#> BAL_29_A1B0 BAL_44b_A0B0 BAL_18_A1B0 BAL_31_A0B1 BAL_45b_A2B0
#> <num> <num> <num> <num> <num>
#> 1: 7.8408 7.5389 7.5057 7.4757 7.7217
#> 2: 6.5479 6.8723 6.7586 6.9175 6.6493
#> 3: 7.8061 7.6090 7.7618 7.5906 7.9382
#> 4: 9.4695 8.8174 9.2959 9.1201 9.1434
#> 5: 4.0921 3.9806 4.0721 4.0626 3.9763
#> ---
#> 22279: 5.5061 5.0290 7.1344 6.3791 5.8032
#> 22280: 4.2469 4.4103 4.5497 4.5338 4.2476
#> 22281: 5.7107 5.4534 6.0937 5.9405 5.4252
#> 22282: 12.5784 12.0046 12.6783 12.7013 12.0769
#> 22283: 12.7121 12.1745 12.7071 12.5966 12.0967
#> BAL_20a_A1B1 BAL_39_A0B1 BAL_47a_A0B0 BAL_37_A1B1 BAL_21_A0B0
#> <lgcl> <num> <num> <num> <num>
#> 1: NA 7.3643 7.7570 7.6151 7.6638
#> 2: NA 6.8158 6.5584 6.7764 6.7385
#> 3: NA 7.4394 7.8905 7.8420 7.5918
#> 4: NA 8.9355 9.0757 9.0833 9.1553
#> 5: NA 4.0417 3.9452 4.0728 4.1046
#> ---
#> 22279: NA 5.6036 5.5698 5.5831 6.2889
#> 22280: NA 4.3762 4.3247 4.2902 4.5706
#> 22281: NA 5.6782 5.3193 5.4597 5.9314
#> 22282: NA 12.6380 12.4291 11.9554 12.2941
#> 22283: NA 12.7395 12.5967 12.0389 12.4245
#> BAL_40_A0B0 BAL_47c_A0B1 BAL_15b_A0B0 BAL_26_A2B0 BAL_42_A0B0
#> <num> <num> <num> <num> <num>
#> 1: 7.6959 7.6721 7.6584 7.3875 7.8968
#> 2: 6.7033 6.8924 6.7241 6.9261 6.6162
#> 3: 7.4063 7.5564 8.0925 8.0984 8.2502
#> 4: 9.2632 9.1023 9.0725 8.8144 9.0405
#> 5: 4.0604 3.9816 3.9857 4.0082 4.1257
#> ---
#> 22279: 5.7738 6.0573 5.6573 5.5300 5.6857
#> 22280: 4.2906 4.4464 4.6204 4.2650 4.3131
#> 22281: 5.5689 5.5811 5.8045 5.3966 5.7005
#> 22282: 12.5281 12.3181 11.8423 12.0778 12.5757
#> 22283: 12.6254 12.3710 12.0150 12.1340 12.5472
#> BAL_12_A1B0 BAL_27b_A2B1 BAL_44a_A0B0 BAL_17_A0B0 BAL_3_A1B0
#> <num> <num> <num> <num> <num>
#> 1: 7.5837 7.5376 7.7166 7.3620 7.6154
#> 2: 7.0007 6.8936 6.9086 6.9581 6.8842
#> 3: 7.5155 7.7496 7.6796 7.7964 7.4748
#> 4: 9.1463 8.9047 9.2588 8.8983 8.9751
#> 5: 4.1134 4.0868 4.0291 4.0442 3.8952
#> ---
#> 22279: 6.2286 5.0878 5.4162 5.8847 5.8753
#> 22280: 4.3363 4.0392 4.6214 4.3300 4.4788
#> 22281: 5.6526 5.1224 6.0406 5.7808 5.6130
#> 22282: 12.4795 12.1495 12.2680 12.2767 12.3744
#> 22283: 12.5716 12.1941 12.3711 12.2172 12.5742
#> BAL_45a_A1B0 BAL_19_A0B0 BAL_33_A0B1 BAL_46_A2B0 BAL_20b_A1B1 BAL_4_A0B0
#> <num> <num> <num> <num> <num> <num>
#> 1: 7.4853 7.6282 7.4844 7.7165 7.6784 7.5597
#> 2: 6.7775 6.8080 7.0474 6.6655 6.6880 6.9416
#> 3: 7.7160 7.8906 7.6490 7.9372 7.8253 7.6235
#> 4: 9.2323 9.1685 8.9928 9.4814 9.2515 9.2566
#> 5: 4.0628 4.0098 4.0483 3.9185 4.0499 4.0568
#> ---
#> 22279: 5.3838 6.5142 5.8302 6.8142 6.8727 5.5462
#> 22280: 4.3461 4.8138 4.3541 4.2114 4.2569 4.4736
#> 22281: 5.3784 6.2741 5.4919 5.8082 5.7742 5.4175
#> 22282: 11.8487 12.3542 11.9772 12.5889 12.5257 12.3581
#> 22283: 11.9828 12.4245 11.9890 12.6001 12.3887 12.5638
#> BAL_47b_A0B1 BAL_15a_A0B1 BAL_25_A0B0 BAL_41_A1B0
#> <num> <num> <num> <num>
#> 1: 7.5602 7.5819 7.5234 7.8389
#> 2: 6.8371 6.7558 6.9205 6.5528
#> 3: 7.8130 7.5988 7.4471 8.0923
#> 4: 9.0188 8.7984 8.9383 9.3820
#> 5: 4.1360 3.9986 3.9627 4.1723
#> ---
#> 22279: 6.6788 5.5957 5.2302 6.2910
#> 22280: 4.5392 4.4584 4.4187 4.4599
#> 22281: 5.6101 5.6350 5.5780 5.5984
#> 22282: 12.7032 12.4696 12.1750 12.1585
#> 22283: 12.7371 12.4656 12.2041 12.1318