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- fixes SomaLogic#81
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stufield committed Jan 29, 2024
1 parent c7a60c3 commit 8f5e527
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Showing 8 changed files with 161 additions and 146 deletions.
3 changes: 3 additions & 0 deletions NAMESPACE
Original file line number Diff line number Diff line change
Expand Up @@ -93,6 +93,7 @@ export(is.apt)
export(is.intact.attributes)
export(is.soma_adat)
export(is_intact_attr)
export(is_lifted)
export(is_seqFormat)
export(left_join)
export(lift_adat)
Expand Down Expand Up @@ -144,6 +145,8 @@ importFrom(dplyr,ungroup)
importFrom(lifecycle,deprecate_soft)
importFrom(lifecycle,deprecate_stop)
importFrom(lifecycle,deprecate_warn)
importFrom(lifecycle,deprecated)
importFrom(lifecycle,is_present)
importFrom(magrittr,"%>%")
importFrom(methods,new)
importFrom(methods,setGeneric)
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6 changes: 0 additions & 6 deletions R/adat-helpers.R
Original file line number Diff line number Diff line change
Expand Up @@ -62,12 +62,6 @@ getAdatVersion <- function(atts) {
}


.ss_ver_map <- c(v3 = "1129", v3.0 = "1129",
v4 = "5k", v4.0 = "5k",
v4.1 = "7k",
v5 = "11k", v5.0 = "11k")


#' Gets the SomaScan version
#'
#' @rdname adat-helpers
Expand Down
141 changes: 50 additions & 91 deletions R/lift-adat.R
Original file line number Diff line number Diff line change
Expand Up @@ -17,9 +17,9 @@
#' Likewise, "lifting" from `v4.0` -> `v4.1` requires
#' a separate annotations file and a `soma_adat` from SomaScan `v4.0`.
#'
#' @param adat A `soma_adat` class object.
#' @param anno.tbl A table of annotations, typically the result of a call
#' to [read_annotations()].
#' @inheritParams params
#' @param bridge The direction of the lift (i.e. bridge).
#' @param anno.tbl Deprecated.
#' @return A "lifted" `soma_adat` object corresponding to the scaling
#' reference in the `anno.tbl`. RFU values are rounded to 1 decimal to
#' match standard SomaScan delivery format.
Expand Down Expand Up @@ -50,19 +50,42 @@
#' attr(lifted, "Header")$HEADER$ProcessSteps
#' attr(lifted, "Header")$HEADER$SignalSpace
#' @importFrom tibble enframe deframe
#' @importFrom lifecycle deprecated is_present
#' @export
lift_adat <- function(adat, anno.tbl) {
lift_adat <- function(adat,
bridge = c("7k_to_5k", "5k_to_7k",
"11k_to_7k", "7k_to_11k"),
anno.tbl = deprecated()) {

stopifnot(inherits(adat, "soma_adat"))
stopifnot(
"`adat` must be a `soma_adat` class object." = inherits(adat, "soma_adat"),
"`adat` must have intact attributes." = is_intact_attr(adat)
)

if ( is_present() ) {
deprecate_warn(
"6.1.0",
"SomaDataIO::lift_adat(anno.tbl =)",
"SomaDataIO::lift_adat(bridge =)",
details = "Passing 'anno.tbl =' is now unnecessary."
)
}

bridge <- match.arg(bridge)
atts <- attr(adat, "Header.Meta")$HEADER
anno_ver <- attr(anno.tbl, "version")
.check_anno(anno_ver)
.check_anml(atts)

# the 'space' refers to the SomaScan assay version signal space
# prefer SignalSpace if present; NULL if absent
from_space <- getSomaScanVersion(adat)
checkSomaScanVersion(from_space)
from_space <- map_ver2k[[from_space]] # map ver to k and strip names
new_space <- .check_direction(from_space, bridge) # check and return new space

if ( grepl("Plasma", atts$StudyMatrix, ignore.case = TRUE) ) {
scalar_col <- ver_dict[[anno_ver]]$col_plasma
ref_vec <- .get_lift_ref(matrx = "plasma", bridge = bridge)
} else if ( grepl("Serum", atts$StudyMatrix, ignore.case = TRUE) ) {
scalar_col <- ver_dict[[anno_ver]]$col_serum
ref_vec <- .get_lift_ref(matrx = "serum", bridge = bridge)
} else {
stop(
"Unsupported matrix: ", .value(atts$StudyMatrix), ".\n",
Expand All @@ -71,92 +94,28 @@ lift_adat <- function(adat, anno.tbl) {
)
}

if ( scalar_col %in% names(anno.tbl) ) {
anno.tbl <- anno.tbl[, c("SeqId", scalar_col)]
} else {
stop(
"Unable to find the required 'Scalar' column in the annotations file.\n",
"Do you have the correct annotations file?",
call. = FALSE
)
}

# the 'space' refers to the assay version signal space
from_space <- atts$SignalSpace # prefer this; NULL if absent
if ( is.null(from_space) ) {
from_space <- atts$AssayVersion # if missing; use this
}

.check_ver(from_space)
.check_direction(scalar_col, from_space)

new_space <- gsub(".*(v[0-9]\\.[0-9])$", "\\1", scalar_col)
attr(adat, "Header.Meta")$HEADER$SignalSpace <- new_space
new_step <- sprintf("Annotation Lift (%s to %s)", tolower(from_space), new_space)
# update attrs with new SignalSpace information
attr(adat, "Header.Meta")$HEADER$SignalSpace <- map_k2ver[[new_space]]
attr(adat, "Header.Meta")$HEADER$AssayVersion <- map_k2ver[[new_space]]
new_step <- sprintf("Lifting Bridge (%s to %s)",
tolower(from_space), new_space)
steps <- attr(adat, "Header.Meta")$HEADER$ProcessSteps
attr(adat, "Header.Meta")$HEADER$ProcessSteps <- paste0(steps, ", ", new_step)
ref_vec <- deframe(anno.tbl)
scaleAnalytes(adat, ref_vec) |> round(1L)
}



# Checks ----
# check attributes of annotations tbl for a version
# x = annotations version from annotations tbl
.check_anno <- function(x) {
if ( is.null(x) ) {
stop("Unable to determine the Annotations file version in `anno.tbl`.\n",
"Please check the attributes via `attr(anno.tbl, 'version')`.",
call. = FALSE)
}
if ( !x %in% names(ver_dict) ) {
stop("Unknown Annotations file version from `anno.tbl`: ", .value(x),
"\nUnable to proceed without knowing annotations table specs.",
call. = FALSE)
}
invisible(NULL)
}

# check that SomaScan data has been ANML normalized
# x = Header attributes
.check_anml <- function(x) {
steps <- x$ProcessSteps
if ( is.null(steps) | !grepl("ANML", steps, ignore.case = TRUE) ) {
stop("ANML normalized SOMAscan data is required for lifting.",
call. = FALSE)
}
invisible(NULL)
}

# check supported versions: v4, v4.0, v4.1
.check_ver <- function(ver) {
allowed <- c("v4", "v4.0", "v4.1")
if ( !tolower(ver) %in% allowed ) {
stop(
"Unsupported assay version: ", .value(ver),
". Supported versions: ", .value(allowed), call. = FALSE
)
}
invisible(NULL)
}

#' @param x the name of the scalar column from the annotations table.
#' @param y the assay version from the adat header information.
#' @noRd
.check_direction <- function(x, y) {
y <- tolower(y)
if ( grepl("4\\.1.*4\\.0", x) & y == "v4" ) {
stop(
"Annotations table indicates v4.1 -> v4.0, however the ADAT object ",
"already appears to be in version ", y, " space.", call. = FALSE
)
}
if ( grepl("4\\.0.*4\\.1", x) & y == "v4.1" ) {
stop(
"Annotations table indicates v4.0 -> v4.1, however the ADAT object ",
"already appears to be in version ", y, " space.", call. = FALSE
)
}
invisible(NULL)
#' Test for lifted objects
#'
#' [is_lifted()] checks whether an object
#' has been lifted (bridged) by the presence
#' (or absence) of the `SignalSpace` entry
#' in the `soma_adat` attributes.
#'
#' @rdname lift_adat
#' @return Logical. Whether `adat` has been lifted.
#' @export
is_lifted <- function(adat) {
x <- attr(adat, "Header.Meta")$HEADER
!is.null(x$SignalSpace)
}
2 changes: 1 addition & 1 deletion R/s3-print-soma-adat.R
Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@ print.soma_adat <- function(x, show_header = FALSE, ...) {
atts_symbol <- if ( attsTRUE ) symb_tick else symb_cross
meta <- getMeta(x)
ver <- getSomaScanVersion(x) %||% "unknown"
ver <- sprintf("%s (%s)", ver, .ss_ver_map[tolower(ver)])
ver <- sprintf("%s (%s)", ver, map_ver2k[tolower(ver)])
n_apts <- getAnalytes(x, n = TRUE)
pad <- strrep(" ", 5L)
dim_vars <- c("SomaScan version", "Attributes intact", "Rows",
Expand Down
Binary file added R/sysdata.rda
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68 changes: 68 additions & 0 deletions R/utils-lift.R
Original file line number Diff line number Diff line change
@@ -0,0 +1,68 @@

# map external commercial names to
# internal SomaScan version names
# ----------------------------------
# 1) bridge 2) lref obj
# ----------------------------------
.bridge_map <- c(
"7k_to_5k" = "v4.1_to_v4.0",
"5k_to_7k" = "v4.0_to_v4.1",
"11k_to_7k" = "v5.0_to_v4.1",
"7k_to_11k" = "v4.1_to_v5.0"
)

map_ver2k <- c(V3 = "112k", v3 = "1129", v3.0 = "1129",
V4 = "5k", v4 = "5k", v4.0 = "5k",
V4.1 = "7k", v4.1 = "7k",
V5 = "11k", v5 = "11k", v5.0 = "11k")

map_k2ver <- c("1129" = "v3.0", "5k" = "v4.0", "7k" = "v4.1", "11k" = "v5.0")

# matrx: either serum or plasma
# bridge: direction of the bridge
.get_lift_ref <- function(matrx = c("plasma", "serum"), bridge) {
matrx <- match.arg(matrx)
bridge <- .bridge_map[bridge]
df <- lref[[matrx]][, c("SeqId", bridge)]
setNames(df[[2L]], df[[1L]])
}


# Checks ----
# check that SomaScan data has been ANML normalized
# x = Header attributes
.check_anml <- function(x) {
steps <- x$ProcessSteps
if ( is.null(steps) | !grepl("ANML", steps, ignore.case = TRUE) ) {
stop("ANML normalized SOMAscan data is required for lifting.",
call. = FALSE)
}
invisible(NULL)
}

#' @param x the 'from' space.
#' @param y the bridge variable, e.g. '5k_to_7k'.
#' @return The 'to' space, from the 'y' param.
#' @noRd
.check_direction <- function(x, y) {
x <- tolower(x)
from <- gsub("(.*)_to_(.*)$", "\\1", y)
to <- gsub("(.*)_to_(.*)$", "\\2", y)

if ( isFALSE(x == from) ) {
stop(
"You have indicated a bridge from ", .value(from),
" space, however your RFU data appears to be in version ",
.value(x), " space.", call. = FALSE
)
}
if ( isTRUE(x == to) ) {
stop(
"You have indicated a bridge to ", .value(to),
" space, however your RFU data already appears to be in ",
.value(x), " space.", call. = FALSE
)
}

invisible(to)
}
24 changes: 20 additions & 4 deletions man/lift_adat.Rd

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