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expand makeGRangesFromDataFrame functionality #32

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052f70f
add helper makeGPosFromDataFrame
LiNk-NY Feb 3, 2020
46f5b82
merge functionality into makeGRangesFromDataFrame
LiNk-NY Feb 4, 2020
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2 changes: 1 addition & 1 deletion R/GPos-class.R
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Original file line number Diff line number Diff line change
Expand Up @@ -176,7 +176,7 @@ GPos <- function(seqnames=NULL, pos=NULL, strand=NULL,
if (is(x_ranges, "IRanges")) # i.e. 'x' is not a GPos
strand <- rep.int(strand, width(x_ranges))
}
if (length(mcols) == 0L && is(x, "GPos"))
if (length(mcols) == 0L && inherits(x, "GenomicRanges"))
mcols <- mcols(x, use.names=FALSE)
if (is.null(seqinfo))
seqinfo <- seqinfo(x)
Expand Down
36 changes: 27 additions & 9 deletions R/makeGRangesFromDataFrame.R
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Expand Up @@ -9,7 +9,6 @@
stop("'", what, ".field' must be a character vector with no NAs")
tolower(field)
}

.collect_prefixes <- function(df_colnames, field)
{
df_colnames_nc <- nchar(df_colnames)
Expand All @@ -29,6 +28,10 @@
idx2 <- which(df_colnames %in% end.field)
if (length(idx1) == 1L && length(idx2) == 1L)
return(list(c(start=idx1, end=idx2), ""))
if (length(idx1) == 1L && length(idx2) == 0L)
return(list(c(start=idx1, end=idx1), ""))
if (length(idx1) == 0L && length(idx2) == 1L)
return(list(c(start=idx2, end=idx2), ""))
if (length(idx1) == 0L && length(idx2) == 0L) {
prefixes1 <- .collect_prefixes(df_colnames, start.field)
prefixes2 <- .collect_prefixes(df_colnames, end.field)
Expand Down Expand Up @@ -74,7 +77,7 @@
.find_strand_col <- function(df_colnames, strand.field, prefix)
{
idx <- which(df_colnames %in% paste0(prefix, strand.field))
if (length(idx) == 0L)
if (length(idx) == 0L)
idx <- which(df_colnames %in% strand.field)
if (length(idx) == 0L)
return(NA_integer_)
Expand All @@ -93,7 +96,7 @@
"chromosome", "chrom",
"chr", "chromosome_name",
"seqid"),
start.field="start",
start.field=c("start", "pos"),
end.field=c("end", "stop"),
strand.field="strand",
ignore.strand=FALSE)
Expand Down Expand Up @@ -144,7 +147,6 @@
ans
}

### 'df' must be a data.frame or DataFrame object.
makeGRangesFromDataFrame <- function(df,
keep.extra.columns=FALSE,
ignore.strand=FALSE,
Expand All @@ -153,12 +155,14 @@ makeGRangesFromDataFrame <- function(df,
"chromosome", "chrom",
"chr", "chromosome_name",
"seqid"),
start.field="start",
start.field=c("start", "pos"),
end.field=c("end", "stop"),
strand.field="strand",
starts.in.df.are.0based=FALSE)
starts.in.df.are.0based=FALSE,
as=c("auto", "GRanges", "GPos"))
{
## Check args.
### 'df' must be a data.frame or DataFrame object.
## Check args.
if (is.character(df)) # for people that provide the path to a file
stop("'df' must be a data.frame or DataFrame object")
if (!(is.data.frame(df) || is(df, "DataFrame")))
Expand All @@ -170,20 +174,26 @@ makeGRangesFromDataFrame <- function(df,
ans_seqinfo <- normarg_seqinfo1(seqinfo)
if (!isTRUEorFALSE(starts.in.df.are.0based))
stop("'starts.in.df.are.0based' must be TRUE or FALSE")
as <- match.arg(as)

granges_cols <- .find_GRanges_cols(names(df),
seqnames.field=seqnames.field,
start.field=start.field,
end.field=end.field,
strand.field=strand.field,
ignore.strand=ignore.strand)

## Prepare 'ans_seqnames'.
ans_seqnames <- df[[granges_cols[["seqnames"]]]]

## Prepare 'ans_ranges'.
ans_start <- .get_data_frame_col_as_numeric(df, granges_cols[["start"]])
ans_end <- .get_data_frame_col_as_numeric(df, granges_cols[["end"]])

if (identical(ans_start, ans_end) && identical(as, "auto"))
as <- "GPos"
else
as <- "GRanges"

if (starts.in.df.are.0based)
ans_start <- ans_start + 1L
ans_names <- rownames(df)
Expand Down Expand Up @@ -229,8 +239,9 @@ makeGRangesFromDataFrame <- function(df,
ans_seqinfo <- Seqinfo(seqlevels)
}

FUN <- switch(as, GRanges = GRanges, GPos = GPos)
## Make and return the GRanges object.
GRanges(ans_seqnames, ans_ranges, strand=ans_strand,
FUN(ans_seqnames, ans_ranges, strand=ans_strand,
ans_mcols, seqinfo=ans_seqinfo)
}

Expand All @@ -242,3 +253,10 @@ setAs("DataFrame", "GRanges",
function(from) makeGRangesFromDataFrame(from, keep.extra.columns=TRUE)
)

setAs("data.frame", "GPos",
function(from) makeGRangesFromDataFrame(from, keep.extra.columns=TRUE)
)

setAs("DataFrame", "GPos",
function(from) makeGRangesFromDataFrame(from, keep.extra.columns=TRUE)
)
15 changes: 15 additions & 0 deletions inst/unitTests/test_makeGRangesFromDataFrame.R
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Original file line number Diff line number Diff line change
Expand Up @@ -152,3 +152,18 @@ test_find_GRanges_cols <- function()
checkIdentical(target, current)
}


test_makeGRangesFromDataFrame <- function()
{
post <- data.frame(chr = rep(1, 3), pos = 11:13)
star <- data.frame(chr = rep(1, 3), start = 11:13)
endo <- data.frame(chr = rep(1, 3), end = 11:13)
checkTrue(validObject(makeGRangesFromDataFrame(post)))
checkTrue(validObject(makeGRangesFromDataFrame(star)))
checkTrue(validObject(makeGRangesFromDataFrame(endo)))

target <- makeGRangesFromDataFrame(data.frame(seqnames=1:6, start=11:16))
checkTrue(validObject(target))
target <- makeGRangesFromDataFrame(data.frame(seqnames=1:6, end=11:16))
checkTrue(validObject(target))
}
2 changes: 1 addition & 1 deletion man/GenomicRangesList-class.Rd
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Original file line number Diff line number Diff line change
Expand Up @@ -89,7 +89,7 @@
}
Note that the \emph{Vector class hierarchy} has many more classes.
In particular \link[S4Vectors]{Vector}, \link[S4Vectors]{List},
\link[IRanges]{RangesList}, and \link[IRanges]{IntegerRangesList}
\link[IRanges]{IRangesList}, and \link[IRanges]{IntegerRangesList}
have other subclasses not shown here.
}

Expand Down
41 changes: 39 additions & 2 deletions man/makeGRangesFromDataFrame.Rd
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,9 @@
\alias{makeGRangesFromDataFrame}

\alias{coerce,data.frame,GRanges-method}
\alias{coerce,data.frame,GPos-method}
\alias{coerce,DataFrame,GRanges-method}
\alias{coerce,DataFrame,GPos-method}

\title{Make a GRanges object from a data.frame or DataFrame}

Expand All @@ -26,10 +28,11 @@ makeGRangesFromDataFrame(df,
"chromosome", "chrom",
"chr", "chromosome_name",
"seqid"),
start.field="start",
start.field=c("start", "pos"),
end.field=c("end", "stop"),
strand.field="strand",
starts.in.df.are.0based=FALSE)
starts.in.df.are.0based=FALSE,
as=c("auto", "GRanges", "GPos"))
}

\arguments{
Expand Down Expand Up @@ -100,6 +103,12 @@ makeGRangesFromDataFrame(df,
start" convention. A notorious example of such resource is the UCSC
Table Browser (\url{http://genome.ucsc.edu/cgi-bin/hgTables}).
}
\item{as}{
A scalar character vector indicating the derivative of
\link{GenomicRanges} object to return, either \link{GRanges} or
\link{GPos}. By default, the derivative will be chosen based on
the data provided (\code{"auto"}).
}
}

\value{
Expand Down Expand Up @@ -177,6 +186,34 @@ makeGRangesFromDataFrame(df, seqinfo=paste0("chr", 4:1))
makeGRangesFromDataFrame(df, seqinfo=c(chrM=NA, chr1=500, chrX=100))
makeGRangesFromDataFrame(df, seqinfo=Seqinfo(paste0("chr", 4:1)))

## GPos objects are returned where appropriate
df <- data.frame(chr="chr1", pos = 11:15, score=1:5)
makeGRangesFromDataFrame(df)

df <- data.frame(chr="chr1", start=11:15, end=11:15,
strand=c("+","-","+","*","."), score=1:5)
makeGRangesFromDataFrame(df)

df <- data.frame(chr="chr1", start=11:15, score=1:5)
makeGRangesFromDataFrame(df)

df <- data.frame(chr="chr1", end=11:15, score=1:5)
makeGRangesFromDataFrame(df)

gr <- makeGRangesFromDataFrame(df, keep.extra.columns=TRUE)
gr2 <- as(df, "GPos") # equivalent to the above
stopifnot(identical(gr, gr2))
gr2 <- GPos(df) # equivalent to the above
stopifnot(identical(gr, gr2))

makeGRangesFromDataFrame(df, ignore.strand=TRUE)
makeGRangesFromDataFrame(df, keep.extra.columns=TRUE,
ignore.strand=TRUE)

makeGRangesFromDataFrame(df, seqinfo=paste0("chr", 4:1))
makeGRangesFromDataFrame(df, seqinfo=c(chrM=NA, chr1=500, chrX=100))
makeGRangesFromDataFrame(df, seqinfo=Seqinfo(paste0("chr", 4:1)))

## ---------------------------------------------------------------------
## ABOUT AUTOMATIC DETECTION OF THE seqnames/start/end/strand COLUMNS
## ---------------------------------------------------------------------
Expand Down