diagnosis.gds: Diagnose the GDS file

In zhengxwen/gdsfmt: R Interface to CoreArray Genomic Data Structure (GDS) Files

Diagnose the GDS file

Description

Diagnose the GDS file and data information.

Usage

diagnosis.gds(gds, log.only=FALSE)

Arguments

gds	an object of class gdsn.class or gds.class
log.only	if TRUE, return a character vector of log only

Value

A list with stream and chunk information.

If gds is a "gds.class" object (i.e., a GDS file), the function returns a list with components, like:

stream	summary of byte stream
log	event log records

If gds is a "gdsn.class" object, the function returns a list with components, like:

head	total_size, chunk_offset, chunk_size
data	total_size, chunk_offset, chunk_size
...

Author(s)

Xiuwen Zheng

Examples

# cteate a GDS file
f <- createfn.gds("test.gds")

set.seed(1000)
rawval <- as.raw(rep(0:99, 50))

add.gdsn(f, "label", NULL)
add.gdsn(f, "raw", rawval)

closefn.gds(f)

##

f <- openfn.gds("test.gds")

diagnosis.gds(f)
diagnosis.gds(f$root)
diagnosis.gds(index.gdsn(f, "label"))
diagnosis.gds(index.gdsn(f, "raw"))

closefn.gds(f)

## remove fragments

cleanup.gds("test.gds")

##

f <- openfn.gds("test.gds")

diagnosis.gds(f$root)
diagnosis.gds(index.gdsn(f, "label"))
(adr <- diagnosis.gds(index.gdsn(f, "raw")))

closefn.gds(f)


## read binary data directly

f <- file("test.gds", "rb")

dat <- NULL
for (i in seq_len(length(adr$data$chunk_offset)))
{
    seek(f, adr$data$chunk_offset[i])
    dat <- c(dat, readBin(f, "raw", adr$data$chunk_size[i]))
}

identical(dat, rawval)  # should be TRUE

close(f)


# delete the temporary file
unlink("test.gds", force=TRUE)

zhengxwen/gdsfmt documentation built on Nov. 19, 2024, 1:03 p.m.