>pheno_data = read.csv("geuvadis_phenodata.csv")
Actually, I dont know how to make the .csv file of my samples. What phenotype information should this csv contain?
I have checked the supplementary data of this research article but didn't find any .csv file.
How I can make the .csv file for my samples to load the phenotype data for ballgown?
Load the phenotype data for the samples. An example file called geuvadis_phenodata.csv is included with the data files for this protocol (ChrX_data). In general, you will have to create this file yourself. It contains information about your RNA sequencing samples, formatted as illustrated in this csv (comma-separated values) file. Each sample should be described on one row of the file and each column should contain one variable. To read this file into R we use the command read.csv. In this file the values are separated by commas, but if the file were tabdelimited you could use the function read.table.
pheno_data = read.csv("geuvadis_phenodata.csv")
- Pertea et al, Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown, Nature Protocols volume 11, pages 1650–1667 (2016)