stuck on the matrix format

[dabitz]

Hi, I am trying to run DiffLogo with your test matrices, but I am not succeeding, most likely by çaking some stupid mistake... Can you help me:

diffLogoFromPwm(pwm1 = "H1-hESC.pwm", pwm2 = "HeLa-S3.pwm")
[1] "pwm must be of class matrix or data.frame. Trying to convert"
[1] "pwm must be of class matrix or data.frame. Trying to convert"
Error in FUN(if (length(d.call) < 2L) newX[, 1] else array(newX[, 1L], :
invalid 'type' (character) of argument
diffLogoFromPwm(pwm1 = "H1-hESC", pwm2 = "HeLa-S3")
[1] "pwm must be of class matrix or data.frame. Trying to convert"
[1] "pwm must be of class matrix or data.frame. Trying to convert"
Error in FUN(if (length(d.call) < 2L) newX[, 1] else array(newX[, 1L], :
invalid 'type' (character) of argument
diffLogoFromPwm(pwm1 = "extdata/pwm/H1-hESC.pwm", pwm2 = "extdata/pwm/HeLa-S3.pwm")
[1] "pwm must be of class matrix or data.frame. Trying to convert"
[1] "pwm must be of class matrix or data.frame. Trying to convert"
Error in FUN(if (length(d.call) < 2L) newX[, 1] else array(newX[, 1L], :
invalid 'type' (character) of argument
Best,
André

[mgledi]

Hey dabitz,
you can not use simple strings. You have to pass PWM-like structures. Have a look at page 7 of https://bioconductor.org/packages/release/bioc/manuals/DiffLogo/man/DiffLogo.pdf.