Re: [R] Reading ASCII files

From: Gabor Grothendieck <ggrothendieck_at_myway.com>
Date: Fri 23 Jul 2004 - 23:02:06 EST

Or assuming that you want snp_id to be character and other columns to have their default class (i.e. ID is numeric, description is factor and genotype is factor) and also assuming that 1st line, etc. is not actually part of the file:

read.table(myfilename, as.is = "snp_id", header = TRUE, fill = TRUE,

   na.string = "")

Liaw, Andy <andy_liaw <at> merck.com> writes:

:
: You can use fill=TRUE and na.string="" in read.table(). E.g.,
:
: > try.dat <- read.table("clipboard", colClasses=rep("character", 6),
: + header=TRUE, fill=TRUE, na.string="")
: > try.dat
: X1st line ID description snp_id genotype
: 1 2nd line 10003 Low rs152240 <NA>
: 2 3rd line 10003 Moderate rs189011 TC
: 3 4th line 10004 Conservative rs152240 GC
: 4 5th line 10004 Bad rs154354 <NA>
: 5 6th line 10013 Bad rs152240 <NA>
: 6 7th line 10019 Conservative rs152240 AC
:
: HTH,
: Andy
:
: > From: Cristian Pattaro
: >
: > Dear all,
: > I need to read an ASCII file with diffent length lines.
: >
: > This is what is contained in the file gene.txt:
: > 1st line ID description snp_id genotype
: > 2nd line 10003 Low rs152240
: > 3rd line 10003 Moderate rs189011 TC
: > 4th line 10004 Conservative rs152240 GC
: > 5th line 10004 Bad rs154354
: > 6th line 10013 Bad rs152240
: > 7th line 10019 Conservative rs152240 AC
: > etc...
: >
: > This is what I would like to obtain in R:
: > ID description snp_id genotype
: > 10003 Low rs152240 NA
: > 10003 Moderate rs189011 TC
: > 10004 Conservative rs152240 GC
: > 10004 Bad rs154354 NA
: > 10013 Bad rs152240 NA
: > 10019 Conservative rs152240 AC
: >
: > Read.table() doesn't work in these situations because of the
: > irregular
: > pattern of data. Have you got any suggestion?
: > Thanks a lot!
: > Cristian
: >
: > ===========================================
: > Cristian Pattaro
: > ===========================================
: >
: > Unit of Epidemiology & Medical Statistics
: > Department of Medicine and Public Health
: > University of Verona
: > cristian <at> biometria.univr.it
: > http://biometria.univr.it
: > ===========================================
: >
: >
: > [[alternative HTML version deleted]]
: >
: > ______________________________________________
: > R-help <at> stat.math.ethz.ch mailing list
: > https://www.stat.math.ethz.ch/mailman/listinfo/r-help
: > PLEASE do read the posting guide!
: > http://www.R-project.org/posting-guide.html
: >
: >
:
: ______________________________________________
: R-help <at> stat.math.ethz.ch mailing list
: https://www.stat.math.ethz.ch/mailman/listinfo/r-help
: PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
:
:



R-help@stat.math.ethz.ch mailing list
https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Fri Jul 23 23:22:14 2004

This archive was generated by hypermail 2.1.8 : Wed 03 Nov 2004 - 22:55:12 EST