Problem copying figures & tab limited files out of R

To copy a figure 

>dev.copy(pdf,"xxx.pdf")
>dev.off()

the pdf can be modified for any other formats too (png, bmp, jpg)

To copy/write table

write.table(file_name,"/PATH/TO/OUTPUT/file.txt",sep="\t")

Hisat2-Ballgown-running error

bg_chrX=ballgown(dataDir="ballgown",samplePattern="xx",pData=pheno_data

The following error can be solved by
check your .csv file when read csv - The order of the samples mentioned must be the same as the order of the samples in the Ballgown folder

Now it will run without any errors

HiSat2 _ R package loading errors

• Error running 

>pheno_data=read.csv("xxx.csv")

place the xxx.csv file in the R bin or wherever R is being executed from

• Error running

>click=ballgown(dataDir=...,samplePattern="...",pData=pheno_data)

run the following before running this command

setwd("/PATH/TO/LIBRARY/") - this path should lead R to identify ballgown, where ballgown is in the folder LIBRARY

• R package 3.4 or other version opens up by default

Download the R-3.2.2 compatible for Hisat2 and run it by routing into the folder R > execute R from its folder and not home directly.