Commit b64a4f61 authored by Holger Brandl's avatar Holger Brandl

print contrasts

parent 41281865
......@@ -67,7 +67,7 @@ vec_as_df(unlist(opts)) %>%
## both batches combines
contrasts = read_tsv(contrasts_file) %T>% kable
contrasts = read_tsv(contrasts_file) %T>% { print(kable(.)) }
expDesign = read_tsv(design_matrix_file) %T>% glimpse
# countData = read_tsv(interp_from_env("../logms_inten_matrix_acc.txt")) %T>% glimpse
countData = read_tsv(count_matrix_file) %T>% glimpse
......@@ -471,7 +471,7 @@ degs %>%
#' Export voom normalization scores per replicate
voomNorm$E %>% as_df %>% rownames_to_column("gene_id") %>%
left_join(geneDescs) %>%
push_left(c("gene_name", "gene_description")) %>%
# push_left(c("gene_name", "gene_description")) %>%
write_tsv(add_prefix("norm_exp_by_replicate.txt"))
......@@ -482,7 +482,7 @@ voomNorm$E %>% as_df %>% rownames_to_column("gene_id") %>%
group_by(condition, gene_id) %>%
summarize(mean_norm_expr = mean(norm_expr)) %>%
left_join(geneDescs) %>%
push_left(c("gene_name", "gene_description")) %>%
# push_left(c("gene_name", "gene_description")) %>%
write_tsv(add_prefix("norm_exp_by_condition.txt"))
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment