Question: replacement has X rows, data has Y rows
0
gravatar for robert_w_link
23 months ago by
robert_w_link0 wrote:

Hello,

I have been using CRISPRseek for a while now, and it has been incredibly useful for my research.

However, an error has been coming up recently for some of my query searches (looking for off-target effects of gRNA templates). When using the following input:

    offTargetAnalysis(inputFilePath = input_path,
                      findgRNAsWithREcutOnly = FALSE,
                      REpatternFile = REpatternFile,
                      findPairedgRNAOnly = FALSE,
                      findgRNAs = FALSE,
                      BSgenomeName = Hsapiens,
                      txd = TxDb.Hsapiens.UCSC.hg19.knownGene,
                      orgAnn = org.Hs.egSYMBOL,
                      max.mismatch = 4,
                      scoring.method = "CFDscore",
                      outputDir = output_dir,
                      overwrite = TRUE)

Some of my queries generate the following output:

>>> Finding all hits in sequence chrUn_gl000249 ...
>>> DONE searching
Building feature vectors for scoring ...
Calculating scores ...
ERROR : replacement has X rows, data has Y

where X < Y.

Here is the output of sessionInfo():

> sessionInfo(package = 'CRISPRseek')
R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
character(0)

other attached packages:
[1] CRISPRseek_1.18.0

loaded via a namespace (and not attached):
[1] compiler_3.4.3  graphics_3.4.3  utils_3.4.3     grDevices_3.4.3
[5] stats_3.4.3     datasets_3.4.3  methods_3.4.3   base_3.4.3
crisprseek • 576 views
ADD COMMENTlink written 23 months ago by robert_w_link0
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