Question: import of kallisto file into R through IsoformswitchanalyzeR
0
gravatar for harry
12 months ago by
harry10
harry10 wrote:

Can anyone tell me the command for importing my kallisto file in R. I am new in this type of work so please suggest me. I use IsoformswitchanalyzeR to import it so please suggest through this command line .

rna-seq • 330 views
ADD COMMENTlink modified 12 months ago by ATpoint36k • written 12 months ago by harry10
0
gravatar for ATpoint
12 months ago by
ATpoint36k
Germany
ATpoint36k wrote:

First hit on google: https://rdrr.io/bioc/IsoformSwitchAnalyzeR/man/importIsoformExpression.html

ADD COMMENTlink written 12 months ago by ATpoint36k

kallistoabundance <- importIsoformExpression(home/aclab/CircRNA/project/kallisto/1/1_AGTCAA_L001_R1_001.out/abundance.tsv ,(package="IsoformSwitchAnalyzeR")) this is correct or not plz tell me becoz it shows error .

ADD REPLYlink written 12 months ago by harry10

shows error is most uninformative. Show it.

ADD REPLYlink written 12 months ago by ATpoint36k

The following commands are i used but i didn't import my file in R please suggest me how i import it.

kallistoQuant <- importIsoformExpression( <-"/home/lab/RNA/kallisto/1/1_AGTCAA_L002_R1_005/" ,(package = " IsoformSwitchAnalyzeR ")) Error: unexpected assignment in "kallistoQuant <- importIsoformExpression( <-"

kallistoQuant <- importIsoformExpression("/home/lab/RNA/kallisto/1/1_AGTCAA_L002_R1_005/" ,(package = " IsoformSwitchAnalyzeR ")) Error in importIsoformExpression("/home/lab/RNA//kallisto/1/1_AGTCAA_L002_R1_005.out/", : Only one of the the 'parentDir' and 'sampleVector' argument can be used.

kallistoQuant <- importIsoformExpression(/home/lab/RNA/kallisto/1/1_AGTCAA_L002_R1_005/ ,(package = " IsoformSwitchAnalyzeR ")) Error: unexpected '/' in "kallistoQuant <- importIsoformExpression(/"

kallistoQuant <- importIsoformExpression(home/lab/RNA/kallisto/1/1_AGTCAA_L002_R1_005 ,(package = " IsoformSwitchAnalyzeR ")) Error: unexpected input in "kallistoQuant <- importIsoformExpression(home/lab/RNA/kallisto/1/1_"

kallistoQuant <- importIsoformExpression(home/lab/RNA/kallisto/1/1_AGTCAA_L002_R1_005 ,(package = " IsoformSwitchAnalyzeR ")) Error: unexpected input in "kallistoQuant <- importIsoformExpression(home/lab/RNA/kallisto/1/1_"

please tell me how to solve it thanks

ADD REPLYlink written 12 months ago by harry10

remove package = " IsoformSwitchAnalyzeR as this is only necessary if using example data from the package. Please get familiar with using R tools and how to generally load data as this does seem to be package-related but is a general R problem.

ADD REPLYlink written 12 months ago by ATpoint36k
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