gravatar for evelyn

2 hours ago by

Hello Everyone,

I want to run linear models in R using salmon output using the TPM values (dependent variable) to check for a possible regression relationship with another independent variable.

I used to import:

dir <- "path of salmon output directory"
list.files(dir)

It lists following salmon output files:

"SRR593_transcripts"
"SRR594_transcripts"
"SRR595_transcripts"
"SRR596_transcripts"
"SRR597_transcripts"
"SRR598_transcripts"
"SRR599_transcripts"
"SRR600_transcripts"

Then I loaded the file for independent variable which looks like:

sample dose
SRR593   0.067
SRR594   0.563
SRR595   4.789
SRR596  10.12
SRR597   12.67
SRR598    0.783
SRR599    5.465
SRR600    6.234

Then to perform linear regression, I want to access TPM values from transcript quant.sf files to do:

model <- lm(TPM ~ dose)

I need help to perform the linear regression part. Thank you in advance!



Source link