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- fixes SomaLogic#81
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Original file line number | Diff line number | Diff line change |
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@@ -0,0 +1,68 @@ | ||
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# 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" | ||
) | ||
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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") | ||
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map_k2ver <- c("1129" = "v3.0", "5k" = "v4.0", "7k" = "v4.1", "11k" = "v5.0") | ||
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# 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]]) | ||
} | ||
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# Checks ---- | ||
# check that SomaScan data has been ANML normalized | ||
# x = Header attributes | ||
.check_anml <- function(x) { | ||
steps <- x$ProcessSteps | ||
if ( is.null(steps) | !grepl("ANML", steps, ignore.case = TRUE) ) { | ||
stop("ANML normalized SOMAscan data is required for lifting.", | ||
call. = FALSE) | ||
} | ||
invisible(NULL) | ||
} | ||
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#' @param x the 'from' space. | ||
#' @param y the bridge variable, e.g. '5k_to_7k'. | ||
#' @return The 'to' space, from the 'y' param. | ||
#' @noRd | ||
.check_direction <- function(x, y) { | ||
x <- tolower(x) | ||
from <- gsub("(.*)_to_(.*)$", "\\1", y) | ||
to <- gsub("(.*)_to_(.*)$", "\\2", y) | ||
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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 | ||
) | ||
} | ||
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invisible(to) | ||
} |
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