[R] Correlation matrix for pearson correlation (r,p,BH(FDR))

[Rainer Schuermann]

The way the sample data is provided is not useful. I have re-built your data, please find the dput() version below (and pls check whether I got it right...).

This is not my area of competence at all, but from what I see from the help page is that the expected parameters are, among others:

x	A matrix or dataframe
y	A second matrix or dataframe __with the same number of rows as x__

I hope that somebody with a better understanding of your intention is able to pick up from here, with the sample data in useful format.

Rgds,
Rainer


dput( genes )
structure(list(Genes = structure(1:10, .Label = c("KCNAB3", "KCNB1", 
"KCNB2", "KERA", "KGFLP1", "KGFLP2", "KHDC1", "KHDC1L", "KHDC3L", 
"KHDRBS1"), class = "factor"), Cell.line1 = c(12.02005181, 0.02457449, 
0.44791862, 0.06090217, 0.02450101, 0, 0, 2.3189445, 0, 0), Cell.line2 = c(11.140091, 
1.3028535, 0.1060137, 0, 0, 0, 0, 2.8252262, 0, 0), Cell.line3 = c(15.60381163, 
0.81538294, 0.09864136, 0.03352993, 0, 0, 0, 5.29099724, 0, 0
), Cell.line4 = c(13.44151596, 0.59318327, 0, 0.03634781, 0, 
0, 0, 7.44183228, 0, 0), Cell.line5 = c(25.3716103, 0.15332321, 
0, 0.04190912, 0, 0, 0, 1.94629741, 0, 0), Cell.line6 = c(8.12373424, 
4.18181234, 0.05857207, 0, 0.02563099, 0, 0, 8.56022436, 0, 0
), Cell.line7 = c(7.67506261, 1.65268403, 0.05945414, 0, 0.03902548, 
0, 0, 7.50838343, 0, 0.0308118), Cell.line8 = c(24.43776341, 
5.9834632, 0.20733924, 0.07752608, 0, 0, 0, 7.17964645, 0, 0), 
    Cell.line9 = c(18.33244818, 1.51423807, 0.05830982, 0.01585643, 
    0, 0, 0, 3.28602729, 0, 0), Cell.line10 = c(9.224225, 0, 
    0, 16.664245, 0, 0, 0, 0, 3.598534, 2.600173)), .Names = c("Genes", 
"Cell.line1", "Cell.line2", "Cell.line3", "Cell.line4", "Cell.line5", 
"Cell.line6", "Cell.line7", "Cell.line8", "Cell.line9", "Cell.line10"
), row.names = c("1", "2", "3", "4", "5", "6", "7", "8", "9", 
"10"), class = "data.frame")

dput( features )
structure(list(Cell.line = c("Growth rate", "Drug sensitivity"
), Cell.line1 = c(NA, "41.33"), Cell.line2 = c(NA, "26.76"), 
    Cell.line3 = c(NA, "24.19"), Cell.line4 = c("51.41", NA), 
    Cell.line5 = c(NA_character_, NA_character_), Cell.line6 = c("5.03", 
    "1.40"), Cell.line7 = c("6.57", "1.88"), Cell.line8 = c("8", 
    "1.33"), Cell.line9 = c("1.26", "5.05"), Cell.line10 = c("3", 
    "9.12")), .Names = c("Cell.line", "Cell.line1", "Cell.line2", 
"Cell.line3", "Cell.line4", "Cell.line5", "Cell.line6", "Cell.line7", 
"Cell.line8", "Cell.line9", "Cell.line10"), row.names = c(NA, 
-2L), class = "data.frame")


On Thu June 18 2015 10:19:55 Sarah Bazzocco wrote:
> This post was called "help" before, I changed the Subject.
> Thanks for the comments.
> Here the example: (I have the two lists saved as .csv and I can open them in R)
> 
> Sheet one- Genes (10 genes expression, not binary, meaured in 10 cell lines)
> > genes
>      Genes  Cell.line1 Cell.line2  Cell.line3  Cell.line4  Cell.line5
> 1   KCNAB3 12.02005181 11.1400910 15.60381163 13.44151596 25.37161030
> 2    KCNB1  0.02457449  1.3028535  0.81538294  0.59318327  0.15332321
> 3    KCNB2  0.44791862  0.1060137  0.09864136  0.00000000  0.00000000
> 4     KERA  0.06090217  0.0000000  0.03352993  0.03634781  0.04190912
> 5   KGFLP1  0.02450101  0.0000000  0.00000000  0.00000000  0.00000000
> 6   KGFLP2  0.00000000  0.0000000  0.00000000  0.00000000  0.00000000
> 7    KHDC1  0.00000000  0.0000000  0.00000000  0.00000000  0.00000000
> 8   KHDC1L  2.31894450  2.8252262  5.29099724  7.44183228  1.94629741
> 9   KHDC3L  0.00000000  0.0000000  0.00000000  0.00000000  0.00000000
> 10 KHDRBS1  0.00000000  0.0000000  0.00000000  0.00000000  0.00000000
>    Cell.line6 Cell.line7  Cell.line8  Cell.line9 Cell.line10
> 1  8.12373424 7.67506261 24.43776341 18.33244818    9.224225
> 2  4.18181234 1.65268403  5.98346320  1.51423807    0.000000
> 3  0.05857207 0.05945414  0.20733924  0.05830982    0.000000
> 4  0.00000000 0.00000000  0.07752608  0.01585643   16.664245
> 5  0.02563099 0.03902548  0.00000000  0.00000000    0.000000
> 6  0.00000000 0.00000000  0.00000000  0.00000000    0.000000
> 7  0.00000000 0.00000000  0.00000000  0.00000000    0.000000
> 8  8.56022436 7.50838343  7.17964645  3.28602729    0.000000
> 9  0.00000000 0.00000000  0.00000000  0.00000000    3.598534
> 10 0.00000000 0.03081180  0.00000000  0.00000000    2.600173
> 
> Sheet two - features (2 features(Growth rate,drug sensitivity for 10 cell lines)
> > features
>          Cell.line Cell.line1 Cell.line2 Cell.line3 Cell.line4 Cell.line5
> 1      Growth rate         NA         NA         NA      51.41         NA
> 2 Drug sensitivity       5.03       6.57          8       1.26          3
>   Cell.line6 Cell.line7 Cell.line8 Cell.line9 Cell.line10
> 1      41.33      26.76      24.19         NA          NA
> 2       1.40       1.88       1.33       5.05        9.12
> 
> What I found:
> corr.test {psych}
> corr.test(x, y = NULL, use = "pairwise",method="pearson",adjust="BH",alpha=.01)
> --> I adjusted the original command to what I need (BH insted og holm) and alpha=.01 insted of 0.05.
> 
> I would be very happy, if someone could show me how to use this command, in particular how to refer as x and y to the two sheets I have (Genes and Features). I would take it from there.
> 
> Thanks a lot in advance.
> 
> Sarah