-
-
Save joowkim/7ffa7a1d6877b99d9db23bc153598bad to your computer and use it in GitHub Desktop.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| library(devtools) | |
| library(sleuth) | |
| library(dplyr) | |
| library("biomaRt") | |
| #load annotation from ensembl | |
| ensembl = useMart("ENSEMBL_MART_ENSEMBL",dataset="mmusculus_gene_ensembl", host="www.ensembl.org") | |
| t2g <- biomaRt::getBM(attributes = c("ensembl_transcript_id", "ensembl_gene_id", "external_gene_name"), mart = ensembl) | |
| t2g <- dplyr::rename(t2g, target_id = ensembl_transcript_id, ens_gene = ensembl_gene_id, ext_gene = external_gene_name) | |
| #change this directory as your directory | |
| base_dir = "/Volumes/Samsung_T1/RNASeq" | |
| sample_id <- dir(file.path(base_dir,"results")) | |
| kal_dirs <- sapply(sample_id, function(id) file.path(base_dir, "results", id)) | |
| kal_dirs <- rev(kal_dirs) | |
| s2c <- read.table(file.path(base_dir,"study_design.txt"), header = TRUE, stringsAsFactors=FALSE) | |
| s2c <- dplyr::select(s2c, sample = run, condition) | |
| s2c <- dplyr::mutate(s2c, path = kal_dirs) | |
| so <- sleuth_prep(s2c, ~ condition, target_mapping = t2g) | |
| so <- sleuth_fit(so) | |
| so <- sleuth_wt(so, which_beta = 'conditionMII') | |
| sleuth_live(so) |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment