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_47c_A0B1 BAL_47b_A0B1 BAL_47a_A0B0 BAL_46_A2B0
#> <char> <num> <num> <num> <num>
#> 1: 780 7.6721 7.5602 7.7570 7.7165
#> 2: 5982 6.8924 6.8371 6.5584 6.6655
#> 3: 3311|3310 7.5564 7.8130 7.8905 7.9372
#> 4: 7849 9.1023 9.0188 9.0757 9.4814
#> 5: 118142757|2978 3.9816 4.1360 3.9452 3.9185
#> ---
#> 22279: 6.0573 6.6788 5.5698 6.8142
#> 22280: 4.4464 4.5392 4.3247 4.2114
#> 22281: 5.5811 5.6101 5.3193 5.8082
#> 22282: 12.3181 12.7032 12.4291 12.5889
#> 22283: 12.3710 12.7371 12.5967 12.6001
#> BAL_45b_A2B0 BAL_45a_A1B0 BAL_44b_A0B0 BAL_44a_A0B0 BAL_43_A0B0
#> <num> <num> <num> <num> <num>
#> 1: 7.7217 7.4853 7.5389 7.7166 7.4546
#> 2: 6.6493 6.7775 6.8723 6.9086 6.9020
#> 3: 7.9382 7.7160 7.6090 7.6796 7.6140
#> 4: 9.1434 9.2323 8.8174 9.2588 9.1342
#> 5: 3.9763 4.0628 3.9806 4.0291 3.9937
#> ---
#> 22279: 5.8032 5.3838 5.0290 5.4162 6.0414
#> 22280: 4.2476 4.3461 4.4103 4.6214 4.3248
#> 22281: 5.4252 5.3784 5.4534 6.0406 5.6337
#> 22282: 12.0769 11.8487 12.0046 12.2680 12.7080
#> 22283: 12.0967 11.9828 12.1745 12.3711 12.7085
#> BAL_42_A0B0 BAL_41_A1B0 BAL_40_A0B0 BAL_4_A0B0 BAL_39_A0B1 BAL_33_A0B1
#> <num> <num> <num> <num> <num> <num>
#> 1: 7.8968 7.8389 7.6959 7.5597 7.3643 7.4844
#> 2: 6.6162 6.5528 6.7033 6.9416 6.8158 7.0474
#> 3: 8.2502 8.0923 7.4063 7.6235 7.4394 7.6490
#> 4: 9.0405 9.3820 9.2632 9.2566 8.9355 8.9928
#> 5: 4.1257 4.1723 4.0604 4.0568 4.0417 4.0483
#> ---
#> 22279: 5.6857 6.2910 5.7738 5.5462 5.6036 5.8302
#> 22280: 4.3131 4.4599 4.2906 4.4736 4.3762 4.3541
#> 22281: 5.7005 5.5984 5.5689 5.4175 5.6782 5.4919
#> 22282: 12.5757 12.1585 12.5281 12.3581 12.6380 11.9772
#> 22283: 12.5472 12.1318 12.6254 12.5638 12.7395 11.9890
#> BAL_31_A0B1 BAL_3_A1B0 BAL_29_A1B0 BAL_27b_A2B1 BAL_27a_A0B0 BAL_26_A2B0
#> <num> <num> <num> <num> <num> <num>
#> 1: 7.4757 7.6154 7.8408 7.5376 7.8763 7.3875
#> 2: 6.9175 6.8842 6.5479 6.8936 6.8416 6.9261
#> 3: 7.5906 7.4748 7.8061 7.7496 7.7334 8.0984
#> 4: 9.1201 8.9751 9.4695 8.9047 9.3388 8.8144
#> 5: 4.0626 3.8952 4.0921 4.0868 4.0015 4.0082
#> ---
#> 22279: 6.3791 5.8753 5.5061 5.0878 5.8953 5.5300
#> 22280: 4.5338 4.4788 4.2469 4.0392 4.4491 4.2650
#> 22281: 5.9405 5.6130 5.7107 5.1224 5.5735 5.3966
#> 22282: 12.7013 12.3744 12.5784 12.1495 12.3097 12.0778
#> 22283: 12.5966 12.5742 12.7121 12.1941 12.3234 12.1340
#> BAL_25_A0B0 BAL_21_A0B0 BAL_20b_A1B1 BAL_20a_A1B1 BAL_19_A0B0
#> <num> <num> <num> <lgcl> <num>
#> 1: 7.5234 7.6638 7.6784 NA 7.6282
#> 2: 6.9205 6.7385 6.6880 NA 6.8080
#> 3: 7.4471 7.5918 7.8253 NA 7.8906
#> 4: 8.9383 9.1553 9.2515 NA 9.1685
#> 5: 3.9627 4.1046 4.0499 NA 4.0098
#> ---
#> 22279: 5.2302 6.2889 6.8727 NA 6.5142
#> 22280: 4.4187 4.5706 4.2569 NA 4.8138
#> 22281: 5.5780 5.9314 5.7742 NA 6.2741
#> 22282: 12.1750 12.2941 12.5257 NA 12.3542
#> 22283: 12.2041 12.4245 12.3887 NA 12.4245
#> BAL_18_A1B0 BAL_17_A0B0 BAL_13_A0B0 BAL_12_A1B0 BAL_1_A0B0 BAL_15b_A0B0
#> <num> <num> <num> <num> <num> <num>
#> 1: 7.5057 7.3620 7.5897 7.5837 7.4623 7.6584
#> 2: 6.7586 6.9581 6.8889 7.0007 7.0674 6.7241
#> 3: 7.7618 7.7964 7.7068 7.5155 7.8392 8.0925
#> 4: 9.2959 8.8983 9.0008 9.1463 9.1243 9.0725
#> 5: 4.0721 4.0442 4.0622 4.1134 4.1629 3.9857
#> ---
#> 22279: 7.1344 5.8847 5.7437 6.2286 6.0442 5.6573
#> 22280: 4.5497 4.3300 4.2274 4.3363 4.3702 4.6204
#> 22281: 6.0937 5.7808 5.4054 5.6526 5.8420 5.8045
#> 22282: 12.6783 12.2767 12.6076 12.4795 12.4001 11.8423
#> 22283: 12.7071 12.2172 12.6159 12.5716 12.4956 12.0150
#> BAL_15a_A0B1 BAL_37_A1B1
#> <num> <num>
#> 1: 7.5819 7.6151
#> 2: 6.7558 6.7764
#> 3: 7.5988 7.8420
#> 4: 8.7984 9.0833
#> 5: 3.9986 4.0728
#> ---
#> 22279: 5.5957 5.5831
#> 22280: 4.4584 4.2902
#> 22281: 5.6350 5.4597
#> 22282: 12.4696 11.9554
#> 22283: 12.4656 12.0389