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Question: could not find function "hash"
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gravatar for joyce
13 months ago by
joyce0
joyce0 wrote:

Hi Julie,

I am using offTargetAnalysis to find gRNAs with CFDscores. I followed the manual and included the subPAM.activity option as follows:

results=offTargetAnalysis("exon.fasta", findgRNAsWithREcutOnly = FALSE, annotateExon = TRUE,findPairedgRNAOnly = FALSE, txdb= txdb, max.mismatch = 3, BSgenomeName = ss, outputDir = ".", overwrite = TRUE,scoring.method="CFDscore", subPAM.activity = hash(AA =0,AC = 0,AG = 0.259259259,AT = 0,CA = 0,CC = 0,CG = 0.107142857,CT = 0,GA = 0.069444444,GC = 0.022222222,GG = 1,GT = 0.016129032,TA = 0,TC = 0,TG = 0.038961039,TT = 0),subPAM.position = c(22, 23),PAM.location = "3prime",mismatch.activity.file = system.file("extdata","NatureBiot2016SuppTable19DoenchRoot.csv",package = "CRISPRseek"))

I encountered the following error message at the score-calculation step:

Error in hash(AA = 0, AC = 0, AG = 0.259259259, AT = 0, CA = 0, CC = 0,  :

  could not find function "hash"

Could you please tell me how to fix this?

Thanks!

ADD COMMENTlink modified 13 months ago by Julie Zhu3.9k • written 13 months ago by joyce0
0
gravatar for Julie Zhu
13 months ago by
Julie Zhu3.9k
United States
Julie Zhu3.9k wrote:
Joyce, Please trying the following command. library("hash") results=offTargetAnalysis("exon.fasta", findgRNAsWithREcutOnly = FALSE, annotateExon = TRUE, annotatePaired = FALSE, findPairedgRNAOnly = FALSE, txdb= txdb, max.mismatch = 3, BSgenomeName = ss, outputDir = ".", overwrite = TRUE,scoring.method="CFDscore") BTW, please include CRISPRseek in the post title next time so that I will not miss your questions. Best, Julie From: "joyce [bioc]" <noreply@bioconductor.org> Reply-To: "reply+01013a1a+code@bioconductor.org" <reply+01013a1a+code@bioconductor.org> Date: Thursday, October 19, 2017 at 7:38 PM To: "Zhu, Lihua (Julie)" <julie.zhu@umassmed.edu> Subject: [bioc] could not find function "hash" Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""> User joyce<https: support.bioconductor.org="" u="" 14189=""/> wrote Question: could not find function "hash"<https: support.bioconductor.org="" p="" 101869=""/>: Hi Julie, I am using offTargetAnalysis to find gRNAs with CFDscores. I followed the manual and included the subPAM.activity option as follows: results=offTargetAnalysis("exon.fasta", findgRNAsWithREcutOnly = FALSE, annotateExon = TRUE,findPairedgRNAOnly = FALSE, txdb= txdb, max.mismatch = 3, BSgenomeName = ss, outputDir = ".", overwrite = TRUE,scoring.method="CFDscore", subPAM.activity = hash(AA =0,AC = 0,AG = 0.259259259,AT = 0,CA = 0,CC = 0,CG = 0.107142857,CT = 0,GA = 0.069444444,GC = 0.022222222,GG = 1,GT = 0.016129032,TA = 0,TC = 0,TG = 0.038961039,TT = 0),subPAM.position = c(22, 23),PAM.location = "3prime",mismatch.activity.file = system.file("extdata","NatureBiot2016SuppTable19DoenchRoot.csv",package = "CRISPRseek")) I encountered the following error message at the score-calculation step: Error in hash(AA = 0, AC = 0, AG = 0.259259259, AT = 0, CA = 0, CC = 0, : could not find function "hash" Could you please tell me how to fix this? Thanks! ________________________________ Post tags: crisprseek You may reply via email or visit could not find function "hash"
ADD COMMENTlink written 13 months ago by Julie Zhu3.9k
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