Thank you very much Peter, Bill and Petr for some great and quite
elegant solutions. There is a lot I can learn from these.
Yes to your question Bill about the raw numbers, they are counts
and they can not be negatives. The data is RNA Sequencing data where
there are approximately 32,000 genes being measured for changes between
two conditions. There are some genes that are not present (can not be
measured) initially, but are present in the second condition, and the
reverse is true also of some genes that are present initially and then
not be present in the second condition (these are often the most
interesting genes). This makes it difficult to compare mathematically
the changes of all genes, so it is common practice to change the 0's to
1's and then redo the log2. 1 is considered sufficiently small, actually
anywhere up to 3 or 5 could be just do to 'background noise' in the
measurement process, but it is somewhat arbitrary.
Matthew
On 7/28/2014 2:43 AM, PIKAL Petr wrote:
Hi
I like to use logical values directly in computations if possible.
yourData[,10] <- yourData[,9]/(yourData[,8]+(yourData[,8]==0))
Logical values are automagicaly considered FALSE=0 and TRUE=1 and can be used
in computations. If you really want to change 0 to 1 in column 8 you can use
yourData[,8] <- yourData[,8]+(yourData[,8]==0)
without ifelse stuff.
Regards
Petr
-----Original Message-----
From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
project.org] On Behalf Of William Dunlap
Sent: Friday, July 25, 2014 8:07 PM
To: Matthew
Cc: r-help@r-project.org
Subject: Re: [R] working on a data frame
if
yourData[,8]==0,
then
yourData[,8]==1, yourData[,10] <- yourData[,9]/yourData[,8]
You could do express this in R as
is8Zero <- yourData[,8] == 0
yourData[is8Zero, 8] <- 1
yourData[is8Zero, 10] <- yourData[is8Zero,9] / yourData[is8Zero,8]
Note how logical (Boolean) values are used as subscripts - read the '['
as 'such that' when using logical subscripts.
There are many more ways to express the same thing.
(I am tempted to change the algorithm to avoid the divide by zero
problem by making the quotient (numerator + epsilon)/(denominator +
epsilon) where epsilon is a very small number. I am assuming that the
raw numbers are counts or at least cannot be negative.)
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Fri, Jul 25, 2014 at 10:44 AM, Matthew
<mccorm...@molbio.mgh.harvard.edu> wrote:
Thank you for your comments, Peter.
A couple of questions. Can I do something like the following ?
if
yourData[,8]==0,
then
yourData[,8]==1, yourData[,10] <- yourData[,9]/yourData[,8]
I think I am just going to have to learn more about R. I thought
getting into R would be like going from Perl to Python or Java etc.,
but it seems like R programming works differently.
Matthew
On 7/25/2014 12:06 AM, Peter Alspach wrote:
Tena koe Matthew
" Column 10 contains the result of the value in column 9 divided by
the value in column 8. If the value in column 8==0, then the
division
can not be done, so I want to change the zero to a one in order to
do the division.".
That being the case, think in terms of vectors, as Sarah says. Try:
yourData[,10] <- yourData[,9]/yourData[,8]
yourData[yourData[,8]==0,10] <- yourData[yourData[,8]==0,9]
This doesn't change the 0 to 1 in column 8, but it doesn't appear
you
actually need to do that.
HTH ....
Peter Alspach
-----Original Message-----
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org]
On Behalf Of Matthew McCormack
Sent: Friday, 25 July 2014 3:16 p.m.
To: Sarah Goslee
Cc: r-help@r-project.org
Subject: Re: [R] working on a data frame
On 7/24/2014 8:52 PM, Sarah Goslee wrote:
Hi,
Your description isn't clear:
On Thursday, July 24, 2014, Matthew
<mccorm...@molbio.mgh.harvard.edu
<mailto:mccorm...@molbio.mgh.harvard.edu>> wrote:
I am coming from the perspective of Excel and VBA scripts, but
I
would like to do the following in R.
I have a data frame with 14 columns and 32,795 rows.
I want to check the value in column 8 (row 1) to see if it is
a 0.
If it is not a zero, proceed to the next row and check the
value
for column 8.
If it is a zero, then
a) change the zero to a 1,
b) divide the value in column 9 (row 1) by 1,
Row 1, or the row in which column 8 == 0?
All rows in which the value in column 8==0.
Why do you want to divide by 1?
Column 10 contains the result of the value in column 9 divided by
the
value in column 8. If the value in column 8==0, then the division
can
not be done, so I want to change the zero to a one in order to do
the division.
This is a fairly standard thing to do with this data. (The data are
measurements of amounts at two time points. Sometimes a thing will
not be present in the beginning (0), but very present at the later
time. Column 10 is the log2 of the change. Infinite is not an easy
number to work with, so it is common to change the 0 to a 1. On the
other hand, something may be present at time 1, but not at the later
time. In this case column 10 would be taking the log2 of a number
divided by 0, so again the zero is commonly changed to a one in
order
to get a useable value in column 10. In both the preceding cases
there was a real change, but Inf and NaN are not helpful.)
c) place the result in column 10 (row 1) and
Ditto on the row 1 question.
I want to work on all rows where column 8 (and column 9) contain a
zero.
Column 10 contains the result of the value in column 9 divided by
the
value in column 8. So, for row 1, column 10 row 1 contains the ratio
column
9 row 1 divided by column 8 row 1, and so on through the whole
32,000
or so rows.
Most rows do not have a zero in columns 8 or 9. Some rows have zero
in column 8 only, and some rows have a zero in column 9 only. I want
to get rid of the zeros in these two columns and then do the
division
to get a manageable value in column 10. Division by zero and Inf are
not considered 'manageable' by me.
What do you want column 10 to be if column 8 isn't 0? Does it
already have a value. I suppose it must.
Yes column 10 does have something, but this something can be Inf or
NaN, which I want to get rid of.
d) repeat this for each of the other 32,794 rows.
Is this possible with an R script, and is this the way to go
about
it. If it is, could anyone get me started ?
Assuming you want to put the new values in the rows where column 8
== 0, you can do it in two steps:
mydata[,10] <- ifelse(mydata[,8] == 0, mydata[,9]/whatever,
mydata[,10]) #where whatever is the thing you want to divide by
that
probably isn't 1 mydata[,8] <- ifelse(mydata[,8] == 0, 1,
mydata[,8])
R programming is best done by thinking about vectorizing things,
rather than doing them in loops. Reading the Intro to R that comes
with your installation is a good place to start.
Would it be better to change the data frame into a matrix, or
something else ?
Thanks for your help.
Sarah
Matthew
--
Sarah Goslee
http://www.stringpage.com
http://www.sarahgoslee.com
http://www.functionaldiversity.org
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