cmapR

cmapR copied to clipboard

This function should support specifying an arbitrary subset of columns to use as reference for computing the median and MAD statistics.

tnat1031

parse_gctx Error: segfault from C stack overflow

13

Hi, i need help to use the parsing function of cmapR I was testing the cmapR library by following the [tutorial](https://bioconductor.org/packages/release/bioc/vignettes/cmapR/inst/doc/tutorial.html) and i have problems with the function parse_gctx when...

FogatoHub

https://github.com/cmap/cmapR/blob/b804d22b701021487591f810045869b98477e089/R/utils.R#L439

tnat1031

right now, the GCT initialize method doesn't do any checking to ensure this if the user passes a predefined rdesc or cdesc object

tnat1031

even when `matrix_only = T`, merge.gct will add metadata of one GCT object to output. Can be fixed by setting cdesc to an empty dataframe as follows, but shouldn't be...

oena

`write.gctx` for incremental output

1

Dear developers, Thanks for developing this software. I wonder if the output function `write.gctx` supports incremental save, so that there is no need to create a GCT object containing full...

luyoutao

don't require 'id' field in rdesc/cdesc for subset.gct

2

tnat1031

for example, when updating cid, this method should handle updating the matrix column names and the id field in cdesc

tnat1031

parse_gctx throwing error which I am not able to understand

3

parse_gctx is not able to read the gct file for me with this command. cmap version is cmapR_1.9.0 . > parse_gctx("BLM_Aged_n83x18577.gct") parsing as GCT v1.2 BLM_Aged_n83x18577.gct NA rows, NA cols,...

jjyotikataria

could not find function parse gctx

1

wangyanmin123