Question: import of kallisto file into R through IsoformswitchanalyzeR
0
gravatar for harry
6 weeks ago by
harry0
harry0 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 • 115 views
ADD COMMENTlink modified 6 weeks ago by ATpoint21k • written 6 weeks ago by harry0
0
gravatar for ATpoint
6 weeks ago by
ATpoint21k
Germany
ATpoint21k wrote:

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

ADD COMMENTlink written 6 weeks ago by ATpoint21k

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 6 weeks ago by harry0

shows error is most uninformative. Show it.

ADD REPLYlink written 6 weeks ago by ATpoint21k

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 6 weeks ago by harry0

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 6 weeks ago by ATpoint21k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 828 users visited in the last hour