On Apr 13, 2012, at 9:08 AM, John Coulthard wrote:
Dear R list people
I loaded a file of numbers into R and got a dataframe of factors.
So I tried to convert it to numeric as per the FAQ using as.numeric().
Actually you used as.numeric(as.character()) which should have been
successful under ordinary circumstances. However you applied it to an
entire dataframe, when you should have applied it to each column
separately. The last error message told you that you were sending the
function the wrong datatype (list).
But I'm getting errors (please see example), so what am I getting
wrong?
Thanks for your time.
John
Example...
#my data object
f
GSM187153 GSM187154 GSM187155 GSM187156 GSM187157 GSM187158
GSM187159
13 7.199346 7.394519 7.466155 8.035864 7.438536 7.308401
7.707994
14 6.910426 6.360291 6.228221 7.42918 7.120322 6.108129
7.201477
15 8.85921 9.152096 9.125067 6.4458 8.600319 8.97577
9.691167
16 5.851665 5.621529 5.673689 6.331274 6.160159 5.65945
5.595156
17 9.905257 8.596643 9.11741 9.872789 8.909299 9.104171
9.158998
18 6.176691 6.429807 6.418132 6.849236 6.162308 6.432743
6.444664
19 7.599871 8.795133 8.382509 5.887119 7.941895 7.666692
8.170374
20 9.458262 8.39701 8.402015 9.0859 8.995632 8.427601
8.265105
21 8.179803 9.868286 10.570601 4.905013 9.488779 9.148336
9.654022
22 7.456822 8.037138 7.953766 6.666418 7.674927 7.995109
7.635158
That is not a reproducible example. You should provide the unedited
output from dput(f)
Try:
numf <- lapply(f, function(x) as.numeric(as.character(x)) ) # returns
a list
numf <- as.data.frame(numf)
str(numf)
'data.frame': 10 obs. of 7 variables:
$ GSM187153: num 7.2 6.91 8.86 5.85 9.91 ...
$ GSM187154: num 7.39 6.36 9.15 5.62 8.6 ...
$ GSM187155: num 7.47 6.23 9.13 5.67 9.12 ...
$ GSM187156: num 8.04 7.43 6.45 6.33 9.87 ...
$ GSM187157: num 7.44 7.12 8.6 6.16 8.91 ...
$ GSM187158: num 7.31 6.11 8.98 5.66 9.1 ...
$ GSM187159: num 7.71 7.2 9.69 5.6 9.16 ...
Tested on
> dput(f)
structure(list(GSM187153 = structure(c(4L, 3L, 8L, 1L, 10L, 2L,
6L, 9L, 7L, 5L), .Label = c("5.851665", "6.176691", "6.910426",
"7.199346", "7.456822", "7.599871", "8.179803", "8.85921", "9.458262",
"9.905257"), class = "factor"), GSM187154 = structure(c(4L, 2L,
9L, 1L, 7L, 3L, 8L, 6L, 10L, 5L), .Label = c("5.621529", "6.360291",
"6.429807", "7.394519", "8.037138", "8.39701", "8.596643", "8.795133",
"9.152096", "9.868286"), class = "factor"), GSM187155 = structure(c(5L,
3L, 10L, 2L, 9L, 4L, 7L, 8L, 1L, 6L), .Label = c("10.570601",
"5.673689", "6.228221", "6.418132", "7.466155", "7.953766", "8.382509",
"8.402015", "9.11741", "9.125067"), class = "factor"), GSM187156 =
structure(c(8L,
7L, 4L, 3L, 10L, 6L, 2L, 9L, 1L, 5L), .Label = c("4.905013",
"5.887119", "6.331274", "6.4458", "6.666418", "6.849236", "7.42918",
"8.035864", "9.0859", "9.872789"), class = "factor"), GSM187157 =
structure(c(4L,
3L, 7L, 1L, 8L, 2L, 6L, 9L, 10L, 5L), .Label = c("6.160159",
"6.162308", "7.120322", "7.438536", "7.674927", "7.941895", "8.600319",
"8.909299", "8.995632", "9.488779"), class = "factor"), GSM187158 =
structure(c(4L,
2L, 8L, 1L, 9L, 3L, 5L, 7L, 10L, 6L), .Label = c("5.65945", "6.108129",
"6.432743", "7.308401", "7.666692", "7.995109", "8.427601", "8.97577",
"9.104171", "9.148336"), class = "factor"), GSM187159 = structure(c(5L,
3L, 10L, 1L, 8L, 2L, 6L, 7L, 9L, 4L), .Label = c("5.595156",
"6.444664", "7.201477", "7.635158", "7.707994", "8.170374", "8.265105",
"9.158998", "9.654022", "9.691167"), class = "factor")), .Names =
c("GSM187153",
"GSM187154", "GSM187155", "GSM187156", "GSM187157", "GSM187158",
"GSM187159"), class = "data.frame", row.names = c("13", "14",
"15", "16", "17", "18", "19", "20", "21", "22"))
class(f)
[1] "data.frame"
#all the columns in the dataframe are of class 'factor'
for(i in 1:ncol(f)){if(class(f[,i])!="factor"){print(class(f[,i]))}}
#but it won't convert to numeric
g<-as.numeric(as.character(f))
Warning message:
NAs introduced by coercion
g
[1] NA NA NA NA NA NA NA NA NA NA
g<-as.numeric(levels(f))[as.integer(f)]
Error: (list) object cannot be coerced to type 'integer'
R version 2.14.1 (2011-12-22)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: i386-redhat-linux-gnu (32-bit)
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West Hartford, CT
______________________________________________
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
