Standard deviation of one column when another column has the same value
Hey guys, I am currently learning different bioinformatics applications, but I do not have all that much of a computer science background. Anyway, I have been asked to perform the mean and standard deviation of coverage for different transcript ID numbers. This involves a huge file with about 30 million lines. Basically, whenever there is the same value in one column/field, I want to get the mean and standard deviation for the other column/field for the corresponding lines. My input and desired output are below, but just imagine there being thousands to millions of different transcript IDs. I also want the output to include all the other fields from the original line for each calculation. The other fields do not follow any special pattern.
So far I have been using a lot of awk, so if you have an awk solution that would be great.
Also if you could give me a formula to next calculate the number of standard deviations each coverage value is away from the mean and put it in a separate field that would be even better, but I think I can figure this part out on my own.
Input
Code:
Transcript ID Other field Other field Coverage
1 3 6 1
2 4 8 2
1 5 10 3
2 6 12 6
Output
Code:
Transcript ID Other field Other field Coverage Mean Standard deviation
1 3 6 1 2 1
2 4 8 2 4 2
1 5 10 3 2 1
2 6 12 6 4 2
Last edited by Scrutinizer; 06-28-2012 at 04:05 AM..
I have a CSV file that looks like
0,0,0,0,1,0,1,0,1,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0
10,11,7,0,4,12,2,3,7,0,11,3,12,4,0,5,5,4,5,0,8,6,12,0,9,3,3,0,2,7,8
19,11,7,0,4,14,16,10,8,2,13,7,15,6,0,76,6,4,10,0,18,10,17,1,11,3,3,0,9,9,8... (7 Replies)
Hi all,
I am new to shell scripting and wanna calculate the mean and standard deviation using shell programming.
I have a file with letters that are repeating and their corresponding duration
a 0.32
a 0.89
aa 0.34
aa 0.23
au 0.012
au 0.26... (4 Replies)
Hi all,
I want to calculate the standard deviation for a column (happens to be column 3).
Does any know of simple awk script to do this?
Thanks (1 Reply)
Hi I want to use awk to print avg and st deviation but it does not go into a file for column 1 only.
I can do average and # of records but i cannot get st deviation.
awk '{sum+=$1} END { print "Average = ",sum/NR}'
thanks (1 Reply)
Hi all,
I need to find the standard deviation of each column of a dataset below for each hour. The data is given in 5 second intervals as shown below
DATE TIME FRAC_DAYS_SINCE_JAN1 FRAC_HRS_SINCE_JAN1 EPOCH_TIME ... (11 Replies)
I have a file with say 50 columns, each containing a whole lot of data.
Each column contains data from a separate simulation, but each simulation is related to the data in the last (REFERENCE) column $50
I need to calculate the RMS deviation for each data line, i.e. column 1 relative to... (12 Replies)
Hi All,
I want someone to modify the below script from this forum so that it can be used for all columns in the file( instead of only printing column 3 mean and standard deviation values). I don't know how to loop around all the columns.
... (3 Replies)
Hi,
I have a file containing 100,000 rows-by-120 columns and I need to compute for the standard deviation for each row. Any idea on how to calculate row-wise standard deviation using awk? My sample data looks like this:
input data:
23 35 12 25 16 17 18 19 29 12
12 26 15 14 15 23 12 12... (2 Replies)
I have a file that looks that this:
820 890 530
1650 1600 1800
1850 1900 2270
1640 2300 1670
2080 2200 2350
1150 1630 2210
I would like to output the mean and standard deviation of each row so that my final output would look like this
820 890 530 746.667 155.849
1650 1600 1800... (5 Replies)
Hello Team,
I am using the following awk script to calculate the SMA (Single Moving Average) for an specific period but now I would like to include the standard deviation output.
Could you please help me to modify this awk shell script
awk -F, -v points=5 ' { a = $2; ... (4 Replies)
Discussion started by: csierra
4 Replies
LEARN ABOUT DEBIAN
font::ttf::coverage
Font::TTF::Coverage(3pm) User Contributed Perl Documentation Font::TTF::Coverage(3pm)NAME
Font::TTF::Coverage - Opentype coverage and class definition objects
DESCRIPTION
Coverage tables and class definition objects are virtually identical concepts in OpenType. Their difference comes purely in their storage.
Therefore we can say that a coverage table is a class definition in which the class definition for each glyph is the corresponding index in
the coverage table. The resulting data structure is that a Coverage table has the following fields:
cover
A boolean to indicate whether this table is a coverage table (TRUE) or a class definition (FALSE)
val A hash of glyph ids against values (either coverage index or class value)
fmt The storage format used is given here, but is recalculated when the table is written out.
count
A count of the elements in a coverage table for use with add. Each subsequent addition is added with the current count and increments
the count.
METHODS
new($isCover [, vals])
Creates a new coverage table or class definition table, depending upon the value of $isCover. if $isCover then vals may be a list of glyphs
to include in order. If no $isCover, then vals is a hash of glyphs against class values.
read($fh)
Reads the coverage/class table from the given file handle
out($fh, $state)
Writes the coverage/class table to the given file handle. If $state is 1 then the output string is returned rather than being output to a
filehandle.
$c->add($glyphid[, $class])
Adds a glyph id to the coverage table incrementing the count so that each subsequent addition has the next sequential number. Returns the
index number of the glyphid added
$c->signature
Returns a vector of all the glyph ids covered by this coverage table or class
@map=$c->sort
Sorts the coverage table so that indexes are in ascending order of glyphid. Returns a map such that $map[$new_index]=$old_index.
$c->out_xml($context)
Outputs this coverage/class in XML
AUTHOR
Martin Hosken Martin_Hosken@sil.org. See Font::TTF::Font for copyright and licensing.
perl v5.10.1 2011-02-25 Font::TTF::Coverage(3pm)