[Bioc-devel] a day in the life of gwascat

Vincent Carey @tvjc @end|ng |rom ch@nn|ng@h@rv@rd@edu
Thu Apr 30 12:54:42 CEST 2020

The EBI GWAS catalog is large -- now the download is over 100MB for 179K
associations.  A "bug" in the
package was reported, so I acquired the file by hand.

> nn = read.delim("gwas_catalog_v1.0.2-associations_e98_r2020-03-08.tsv",

*Warning message:*

*In scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  :*

*  EOF within quoted string*

> dim(nn)

[1] 35264    38

The "bug" is the number 35264 ...


[1]+  Stopped                 R

%vjcair> wc gwas_cat*tsv

  179365 13243516 120140148

%vjcair> vi gwas_cat*tsv

%vjcair> fg


> tail(nn)

*Error: C stack usage  98161262 is too close to the limit*

*Maybe my R needs to be updated.*

*If I use data.table::fread to consume the tsv over HTTP all seems well,
and perhaps*

*I will switch to that.*

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