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add method glmmTMB #296

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merged 13 commits into from
Sep 17, 2023
Merged

add method glmmTMB #296

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ea09c13
add method glmmTMB
stemangiola Sep 14, 2023
846a201
relax tests
stemangiola Sep 14, 2023
8bf8dba
fix :::
stemangiola Sep 14, 2023
e41a952
add dependency
stemangiola Sep 14, 2023
24673bd
add internal function
stemangiola Sep 14, 2023
f65d233
fix bug for tmb for gene4s with error
stemangiola Sep 15, 2023
0b395c4
avoid complete failure if vcov is NaN
stemangiola Sep 16, 2023
8bcd08a
unrelated details, use abundance for reduce dimension
stemangiola Sep 17, 2023
69d6d33
add dependency
stemangiola Sep 17, 2023
20c8fb5
add glmmSeq class
stemangiola Sep 17, 2023
a276b5a
add class detals
stemangiola Sep 17, 2023
be1f5c6
add summary method
stemangiola Sep 17, 2023
a02224b
fix dependencies
stemangiola Sep 17, 2023
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1 change: 1 addition & 0 deletions DESCRIPTION
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Expand Up @@ -83,6 +83,7 @@ Suggests:
pbapply,
pbmcapply,
lme4,
glmmTMB,
MASS
VignetteBuilder:
knitr
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1 change: 1 addition & 0 deletions NAMESPACE
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Expand Up @@ -172,6 +172,7 @@ importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,na.omit)
importFrom(stats,p.adjust)
importFrom(stats,pchisq)
importFrom(stats,plogis)
importFrom(stats,prcomp)
importFrom(stats,qlogis)
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16 changes: 8 additions & 8 deletions R/functions.R
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Expand Up @@ -693,7 +693,7 @@ get_differential_transcript_abundance_glmmSeq <- function(.data,
.abundance = enquo(.abundance)
.sample_total_read_count = enquo(.sample_total_read_count)
.dispersion = enquo(.dispersion)

# Check if omit_contrast_in_colnames is correctly setup
if(omit_contrast_in_colnames & length(.contrasts) > 1){
warning("tidybulk says: you can omit contrasts in column names only when maximum one contrast is present")
Expand Down Expand Up @@ -757,33 +757,33 @@ get_differential_transcript_abundance_glmmSeq <- function(.data,

# Reorder counts
counts = counts[,rownames(metadata),drop=FALSE]

if(quo_is_symbolic(.dispersion))
dispersion = .data |> pivot_transcript(!!.transcript) |> select(!!.transcript, !!.dispersion) |> deframe()
else
dispersion = setNames(edgeR::estimateDisp(counts)$tagwise.dispersion, rownames(counts))

# # Check dispersion
# if(!names(dispersion) |> sort() |> identical(
# rownames(counts) |>
# sort()
# )) stop("tidybulk says: The features in the dispersion vector do not overlap with the feature in the assay")

# Make sure the order matches the counts
dispersion = dispersion[rownames(counts)]
glmmSeq_object =

glmmSeq_object =
glmmSeq( .formula,
countdata = counts ,
metadata = metadata,
dispersion = dispersion,
progress = TRUE,
progress = TRUE,
method = method |> str_remove("(?i)^glmmSeq_"),
...
)

glmmSeq_object |>
summary() |>
summary_lmmSeq() |>
as_tibble(rownames = "gene") |>
mutate(across(starts_with("P_"), list(adjusted = function(x) p.adjust(x, method="BH")), .names = "{.col}_{.fn}")) |>

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2 changes: 1 addition & 1 deletion R/functions_SE.R
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Expand Up @@ -1158,7 +1158,7 @@ get_differential_transcript_abundance_glmmSeq_SE <- function(.data,
)

glmmSeq_object |>
summary() |>
summary_lmmSeq() |>
as_tibble(rownames = "transcript") |>
mutate(across(starts_with("P_"), list(adjusted = function(x) p.adjust(x, method="BH")), .names = "{.col}_{.fn}")) |>

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