Skip to content

Fix deseq contrasts #114

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 3 commits into from
Sep 26, 2020
Merged

Fix deseq contrasts #114

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
65f1130
select the right default contrast in deseq2
stemangiola Sep 26, 2020
7c6ec28
drop levels in the correct way
stemangiola Sep 26, 2020
41ea96a
fix some checks
stemangiola Sep 26, 2020
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
59 changes: 23 additions & 36 deletions R/functions.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -321,7 +321,7 @@ get_differential_transcript_abundance_bulk <- function(.data,
distinct() %>%

# drop factors as it can affect design matrix
mutate_if(is.factor, as.character())
droplevels()
#%>%

# # Check if data rectangular
Expand Down Expand Up @@ -537,7 +537,7 @@ get_differential_transcript_abundance_bulk_voom <- function(.data,
distinct() %>%

# drop factors as it can affect design matrix
mutate_if(is.factor, as.character())
droplevels()
# %>%

# # Check if data rectangular
Expand Down Expand Up @@ -743,15 +743,7 @@ get_differential_transcript_abundance_deseq2 <- function(.data,
distinct() %>%

# drop factors as it can affect design matrix
mutate_if(is.factor, as.character()) %>%

# # Check if data rectangular
# ifelse2_pipe(
# (.) %>% check_if_data_rectangular(!!.sample,!!.transcript,!!.abundance) %>% not() & fill_missing_values,
# (.) %>% check_if_data_rectangular(!!.sample,!!.transcript,!!.abundance) %>% not() & !fill_missing_values,
# ~ .x %>% fill_NA_using_formula(.formula,!!.sample, !!.transcript, !!.abundance),
# ~ .x %>% eliminate_sparse_transcripts(!!.transcript)
# ) %>%
droplevels() %>%

# Needed for DESeq2
mutate(!!.abundance := as.integer(!!.abundance)) %>%
Expand All @@ -770,25 +762,27 @@ get_differential_transcript_abundance_deseq2 <- function(.data,
deseq2_object %>%

# If I have multiple .contrasts merge the results
ifelse_pipe(
my_contrasts %>% is.null | omit_contrast_in_colnames,

when(

# Simple comparison
~ .x %>%

(my_contrasts %>% is.null | omit_contrast_in_colnames) & (deseq2_object@colData[,parse_formula(.formula)[1]] %>% class %in% c("numeric", "integer", "double")) ~
(.) %>%
DESeq2::results() %>%
as_tibble(rownames = quo_name(.transcript))
# %>%

# # Mark DE genes
# mutate(significant = padj < significance_threshold) %>%

# # Arrange
# arrange(padj),

# Multiple comparisons
as_tibble(rownames = quo_name(.transcript)),

# Simple comparison
my_contrasts %>% is.null | omit_contrast_in_colnames ~
(.) %>%
DESeq2::results(contrast = c(
parse_formula(.formula)[1],
deseq2_object@colData[,parse_formula(.formula)[1]] %>% levels %>% .[2],
deseq2_object@colData[,parse_formula(.formula)[1]] %>% levels %>% .[1]
)) %>%
as_tibble(rownames = quo_name(.transcript)),

# Multiple comparisons NOT USED AT THE MOMENT
~ {
deseq2_obj = .x
deseq2_obj = (.)

1:ncol(my_contrasts) %>%
map_dfr(
Expand All @@ -800,21 +794,13 @@ get_differential_transcript_abundance_deseq2 <- function(.data,
# Convert to tibble
as_tibble(rownames = quo_name(.transcript)) %>%
mutate(constrast = colnames(my_contrasts)[.x])
# %>%
#
# # Mark DE genes
# mutate(significant = padj < significance_threshold)

) %>%
pivot_wider(values_from = -c(!!.transcript, constrast),
names_from = constrast, names_sep = "___")
}
) %>%

# # Add filtering info
# right_join(.data %>% distinct(!!.transcript)) %>%
# when(!"lowly_abundant" %in% colnames(.data) ~ (.) %>% mutate(lowly_abundant = if_else(is.na(log2FoldChange), T, F)) ,
# ~ (.)) %>%

# Attach prefix
setNames(c(
colnames(.)[1],
Expand All @@ -827,6 +813,7 @@ get_differential_transcript_abundance_deseq2 <- function(.data,

# Add raw object
attach_to_internals(deseq2_object, "DESeq2") %>%

# Communicate the attribute added
{
message(
Expand Down
8 changes: 4 additions & 4 deletions tests/testthat/test-bulk_methods.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -524,7 +524,7 @@ test_that("DESeq2 differential trancript abundance - no object",{
res_deseq2 =
test_deseq2_df %>%
DESeq2::DESeq() %>%
results()
DESeq2::results()

res_tidybulk =
test_deseq2_df %>%
Expand Down Expand Up @@ -552,7 +552,7 @@ test_that("DESeq2 differential trancript abundance - no object",{

expect_equal(
unique(res$log2FoldChange)[1:4],
c(-12.322037, -11.670005 , -9.048954 ,-12.603183),
c(3.449740, 2.459516, 2.433466, 1.951263),
tolerance=1e-6
)

Expand Down Expand Up @@ -580,7 +580,7 @@ test_that("DESeq2 differential trancript abundance - no object",{

expect_equal(
unique(res$log2FoldChange)[1:4],
c(-3.656244 ,-3.241215, -3.037658, 4.173217),
c(-1.1906895, -0.4422231, 0.9656122, -0.3328515),
tolerance=1e-6
)

Expand All @@ -605,7 +605,7 @@ test_that("DESeq2 differential trancript abundance - no object",{

expect_equal(
unique(res$log2FoldChange)[1:4],
c(-10.432623, -6.747017, -7.598174 , 6.598429),
c(1.1110210, 3.0077779, 0.9024256, 4.7259792),
tolerance=1e-6
)

Expand Down
2 changes: 1 addition & 1 deletion vignettes/manuscript_transcriptional_signatures.Rmd
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ vignette: >
%\usepackage[UTF-8]{inputenc}
---

This decument includes the code used for the manuscript, for the transcriptional signature identification.
This document includes the code used for the manuscript, for the transcriptional signature identification.


```{r, echo=FALSE, include=FALSE}
Expand Down