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hyunhwan-jeong / CB2

CB2 is an R package which provides functions for hit gene identification and quantification of sgRNA (single-guided RNA) abundances for CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) pooled screen data analysis. Details are in Jeong et al. (2019) <doi:10.1101/gr.245571.118> and Baggerly et al. (2003) <doi:10.1093/bioinformatics/btg173>.
https://cran.r-project.org/web/packages/CB2/index.html
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Error in measure_gene_stats(sgrna_stat) #18

Open suderis opened 1 year ago

suderis commented 1 year ago

Hi I am trying to get gene stats from the code but ı get this following error;


Error in measure_gene_stats(sgrna_stat) : 
  It looks like `sgrna_stat` does not contain any result of a statistical test.

I used the counts from MAGeCK produced to code but all the format is appropriate with CB2 format. How can I fix this issue? The sgRNA stats worked perfectly.

Thanks in advance

hyunhwan-jeong commented 1 year ago

Hi, could you share what you put to sgrna_stat? Thank you

suderis commented 1 year ago

`sgrna_stat <- measure_sgrna_stats(J82_count, df_design,group_a = "T0",groupb = "G",delim = "",ge_id = "Gene",sg_id = "sgRNA")

head(sgrna_stat) Gene sgRNA n_a n_b phat_a vhat_a phat_b vhat_b cpm_a cpm_b 1 COL15A1 sgCOL15A1_2 1 3 1.831101e-05 0 2.158151e-05 3.582704e-13 18.31101 22.17798 2 LACC1 sgLACC1_1 1 3 1.675262e-05 0 1.862168e-05 3.459494e-12 16.75262 18.57624 3 BOD1L1 sgBOD1L1_3 1 3 1.465855e-05 0 1.632593e-05 2.691174e-11 14.65855 16.32042 4 ITFG1 sgITFG1_1 1 3 2.873270e-06 0 1.092631e-05 5.610771e-12 2.87327 10.88184 5 KCTD16 sgKCTD16_2 1 3 2.459324e-05 0 2.277680e-05 3.781127e-13 24.59324 24.60295 6 ADD3 sgADD3_1 1 3 1.090869e-05 0 1.185389e-05 2.556015e-11 10.90869 11.84388 logFC t_value df p_ts p_pa p_pb fdr_ts fdr_pa fdr_pb 1 0.2633311870 5.4639798 2 0.03190101 0.98404950 0.01595050 0.1001397 0.9997659 0.1503497 2 0.1410711114 1.0048866 2 0.42077345 0.78961327 0.21038673 0.5329416 0.9997659 0.5300289 3 0.1455238811 0.3214133 2 0.77837816 0.61081092 0.38918908 0.8370835 0.9997659 0.8109563 4 1.6171339532 3.3997608 2 0.07669632 0.96165184 0.03834816 0.1780190 0.9997659 0.2326820 5 0.0005473835 -2.9540115 2 0.09803526 0.04901763 0.95098237 0.2077280 0.1735382 0.9999973 6 0.1090668677 0.1869572 2 0.86894153 0.56552923 0.43447077 0.9079486 0.9997659 0.8791015`

hyunhwan-jeong commented 1 year ago

have you resolved the problem? otherwise, could you send the r object to jeong.compbio@gmail.com?

Thank you,